What the Hell Happened Here !
by The Sithspawn
Summary: FarscapeThe Matrix crossover: John Crichton returns to Earth after being gone for centuries but Earth isn't as he remembered it.
1. Prelude

What the Hell happened Here?!

Farscape/The Matrix crossover

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Disclaimer: I do not own Farscape or The Matrix and am making no money off of this.

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Concerning Events: In the Farscape universe 100 years have past since the destruction of Katrazi. Kansas, Terra Firma and Bad Timing did not occur.

In The Matrix universe this is set after the first movie and is AU the other movies will not occur in this story.

Prelude: 

John Crichton stood on the Observation deck of his Command Carrier watching the stars go by and his rattlers were in **OVERDRIVE. **Even more than before that eventful day 100 cycles ago.

After all these cycles, he was finally going Home.

After over a century away from Earth from his perspective, he was finally going home, boy were they going to be surprised. He should have been dead by now but thanks to some of Scorpy's experiments, John could now boast of a Sebacean life expectancy AT LEAST, if not more. He had to admit a lot a good things had come out of that; more time with Aeryn and their children and their children's children. Not to mention he got to be there for Leslie (Katralla's daughter).

Looking back over the years, things had really changed. He had gone from being the most wanted and feared sentient in the Uncharted Territories to Grand Admiral and Supreme Commander of the Fleet for the United Multi-Species Hegemony. Hell, kids of all ages and all species wanted to grow up become just like him. Wherever he went now he was welcomed and his presence was honored with diplomatic parties and such instead of being welcomed with open pulse pistols and firefights. Though there were times when he missed the action and other's where he just wanted to pull out Wynona and start shooting everyone and everything in sight.

**There's only so much diplomatic bickering a guy can take without losing it. **

And Humanity to all the other races had taken on a mythical air. Everywhere he went people wanted to know about Earth and it's peoples and whether everyone there was just like him.

Though it wasn't all fun'n'games all the time, there had been some really bad times fighting off the Scarrens and Nebari, rebelling against Peacekeeper Command and chasing the Sheyangs. Sure he'd won all of those but it was close in a lot of them, really really close when it came to the Nebari, their plague had been something else.

And Now…

He was in the Sol system.

Going Home.

100 cycles too late to see dad, DK, Olivia, Susan or anyone else he had left behind.

To make matters worse intercepted radio signals from Earth indicated that another one or two centuries had also passed, at least; meaning that frelling wormhole had dilated time as well and didn't just through him across the galaxy.

**__**

There was no one left for him on Earth.

…………………

There was Jupiter just passing them by, damn it was BIG. Few systems had gas giants this big. The techs were prepping a special Marauders for a detailed up close scan of the planet.

In a few arns they would be in Earth orbit. They could have been there in less time but he didn't want to scare the natives by appearing suddenly. In another arn the stealth prowlers he'd sent to scan Earth would be back and then he would decide how to handle First contact.

John Crichton stood alone on the observation deck pondering what he was going to do and what he was about to drop in Humanities collective lap.

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1 Arn later

"Bridge to Admiral Crichton"

"Crichton here"

"Admiral the prowlers have returned and .....their preliminary findings are in," stuttered his normally phlegmatic Kalish communications officer

John cocked his head, " And?"

"Sir, it would be best if you come to the bridge and see the results for yourself"

"Just spit it , What's WRONG?"

"Sir..."

"WELL?"

"It's just that...."

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"JUST SAY IT ," John yelled.

"They report **NO **artificial satellites in orbit , 1 derelict space station and ....." the officer hesitated.

"WHAT ELSE ?"

"Cloud coverage is 100"

John didn't say a thing. He didn't need to, everyone knew what that meant. No Sunlight reaching the surface, No plant growth.

**__**

Earth might as well have been a lifeless airless moon.

"Sir ?"

It was a few microts before John could answer.

"Something else?"

"Yes sir, massive EM emissions were registered"

John thought about it for a moment. EM emissions meant someone could still be alive down there.

"Have Helm set course for Earth maximum speed, I'll be on the bridge shortly"

"Yes sir, .... our ETA is 500 micots."

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Author's notes: Hope u like the prelude. Feedback is Appreciated.


	2. Chapter 1 Contemplations

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What the Hell Happened Here!?

Disclaimer: see chapter 1

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Author's notes: Thanks for the feedback. Ideas for future chapters are appreciated.

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Chapter One: Contemplations

John Crighton's mind had been like a churning ocean with the primary report about Earth being the tsunami that had started all the churning. Here he was heading for the bridge contemplating the probable fact the he was _the last surviving member of the human race._

John shuddered

He really, _really_ didn't like that _thought_.

Hell, he'd prefer to go back to being the most wanted man in the Uncharted Territories with Scorpious only half a step behind him.

The only thing that had kept the news from totally breaking him was the fact that the marauder patrol had picked massive EM emissions underneath the cloud coverage.

He hadn't felt this overwhelmed since the responsibility of being Supreme Commander had been through into his lap all those years ago.

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This was a whole new can of worms.

**__**

One he sincerely wished he hadn't opened.

He reached the bridge and entered. What he found was something that could only be described as the controlled chaos that was his _bridge_, and standing in the middle of it was Admiral Aeryn Sun-Crichton.

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His wife.

They had finally gotten their act together after the destruction of Katrazi. And here they were; the best Husband and Wife team this side of the Galactic Core. They'd stuck together through thick and thin, endured all the separations the wars had forced on them and still managed to have a family. A BIG family. A really BIG family.

For the first 20 cycles of their marriage they had managed to have a child nearly every two cycles. After that, it was nearly once every ten years with the help of a large amount of contraceptives (the medics still could not believe how much they used in a single year). They'd learned that it was best to have a child old enough to help look after the newborn. That was not to say that they had not had offers to help, from all their friends. Chiana and Jool had always been there to help them and after he'd become supreme commander, the nursery nannies on his ship had been falling over each over to give them a helping hand. So, after 100 cycles of marriage they had 18 kids (not including Leslie; Katralla's daughter) with the youngest only 6 cycles old and Aeryn pregnant and expecting to give birth in a matter of days.

She was very swollen but she had insisted on taking command under him while the mission to Earth was ongoing.

**__**

She'd wanted to give birth on Earth.

It didn't look like she was going to get her wish.

The officers of the bridge finally took notice of the admiral standing there lost in thought. The bridge became deathly silent. You could have heard a pin drop. All the officers were worried about the admiral and how he was reacting to the preliminary reports they had received. All of them had worried expressions painted on their faces, while Aeryn had a pained expression on her face.

"Report," commanded John

"The marauders have returned and are docking now, as soon as the are finished they will report directly to the bridge to give you their full report," answered Aeryn

"Good I'll be in my Ready Room," and with a curt nod he walked to his Ready Room.

The captain's Ready Room was added in the first redesign (at John's request) of the bridge of all the first generation UMSH command carriers. It was similar to the old observation area in the old Peacekeeper carriers but with a few improvements. This included a personal bathroom, a comfortable desk for the captain to work on plus the widow that overlooked the bridge was replaced with a one way mirror that can act as a view screen for small private meetings.

It had been John's idea to add a just like on Picard's _Enterprise_. Over the years he had quietly inserted into the Hegemony Navy small things that reminded him of home as a sort of insider's joke that only he knew of. Things like yellow and red alerts from Star Trek, human names for ships like Enterprise and Home one, and he had even introduced callsigns to the fighter pilot corps of the Navy.

John reached his desk and collapsed into his chair, wondering what was going to happen next.

The door to his Ready Room opened and in waddled Aeryn. She pulled up a chair next to him and sat down. She reached out and took his hand.

The sat in silence.

Finally, Aeryn said, "You need to talk John,"

"I know Sunshine, just not right now…First we find out what happened then I'll deal."

Aeryn tightly squeezed his hand, "You don't have to keep everything inside, I'm here for you just as you've always been there for me."

Together they sat in silence wondering what was going to happen **_next._**

Hoping that everything would turn out okay, as it always had.

Author's Notes: Here's the next chapter. Sorry its so short, I'm still working out what happens next, please be patient with me. As always feedback is appreciated.


	3. Chapter 2 Reports and Decisions

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What the Hell happened here!

Disclaimer: I don't own the Matrix or Farscape

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Author's notes: Your reviews were appreciated.

Chapter 2 Reports and Decisions

An extremely nervous Delvian marauder lieutenant walked into the admiral's ready room, saluted and stood ready to give his report to the admiral. John could visibly see the lieutenant swaying were he stood while nervously swallowing.

"Well lieutenant Sar, what do you have to report?" asked John with dread in his heart.

The lieutenant swallowed and hesitantly started, "Admiral…we approached _the planet_ at minimum speed and maximum stealth as per your orders and proceeded to scan _the planet_.No artificial satellites registered on sensors. Visual examination of _the planet_ showed above average cloud cover for the hemisphere that was visible to us. Upon further examination of the rest of _the planet,_ it was discovered that cloud coverage was **_total _**, we proceeded to scan the clouds and discovered that this was _not a natural occurrence_. It appears that this was the result of some type of weapon , unknown to us. It appears that the clouds are in almost continuous turmoil indicting constant storms underneath the cloud coverage. In addition, the cloud coverage is apparently constant for the entire globe. Radiation readings from the clouds indicted that they have been this way for _hundreds of cycles,_" the Lieutenant shuddered at the thought of a planet without sunlight, as a plant this idea was specifically repellent, to say the least.

The lieutenant stopped to catch his breath while continuously, nervously shifting from one foot to another before continuing, "On further orbits of _the planet_ , we came across a derelict space station. No life signs registered on sensors. It appeared to have been abandoned for a period of time since before cloud coverage was complete."

John felt everything come loose inside of him. It took every ounce of John's willpower not to collapse or breakdown into tears. If not for Aeryn's supporting presence next to him he would have. John took several breaths then stared up at the lieutenant. The lieutenant flinched from the admiral's gaze. John evenly said through clenched teeth, "Anything else? Didn't your initial report state that your sensors registered EM emissions from the planets surface?"

"Ah …yes sir. I was just about to bring that up sir. We entered the outer atmosphere of _the planet_ at which time we began registering massive EM emissions…Sir the readings were off the scale, more than that of twenty _Talyn_-class Command Carriers. Sir…this was **_only in ONE spot_**. These readings were repeated in other hot spots spread over a large portion of the surface of _the planet_." The lieutenant continued nervously, "After we discovered this we…I decided to return to the ship for further orders."

"Why ?" cut in Aeryn

Lieutenant Sar turned to face Aeryn, "One of my officers mentioned the possibility of these EM emissions being some type of offensive weapon and…frankly admiral, I wouldn't want to be on the receiving end of such a weapon," explained an ashen faced Lieutenant.

"How many 'hot spots' did your sensors register?" inquired Aeryn.

The lieutenant grimaced then answered, "We registered,"-gulp-"**_thousands_**."

John just looked at the lieutenant realizing now why the lieutenant was so afraid.

**__**

Earth was giving off enough energy to be mistaken for a small sun.

Suddenly the situation on Earth did not seem as dire as John had thought.

If they can generate that much energy without sunlight than there must be some type of civilization down there, thought a relived John.

**__**

I'm not the last human in the universe, was John's triumphant thought.

"Is that all lieutenant ?" asked Aeryn.

"Yes ma'am"

"Then you're dismissed."

"Aye ma'am." The lieutenant saluted and left John and Aeryn alone to ponder what his report meant.

The churning in John's mind and stomach had calmed down a great deal, but still he was uneasy…localized areas giving off energy readings equal to twenty Talyn-class Command Carriers! The Talyn-class had been the new class of Command Carriers that had come into service for the UMSH during the Nebari War. They were the largest class of ships serving in the fleet. They were four times the size of the old Peacekeeper Command Carriers and with more weaponry than an equal number of those old carriers. This much energy generation was unheard of on a planetary scale. These types of readings were more likely to be registered when scanning quantum singularities and stars…_not when scanning planets_.

For an eternity after the lieutenant left, they remained silent. Relief that had washed over John when heard about the energy readings had vanished now that he had time to think it over.

If they can generate that much energy, why can't they clear the cloud coverage?

This thought was repeated over and over again in his mind while he tried to consider what all this really meant.

__

Something isn't right.

He could feel it in his bones.

Finally, Aeryn broke the silence; "You heard the report, what do you think the energy readings represent?"

"Not a weapon. You know how paranoid my planet is. If it were a weapon, they would have used it to blow the marauders out of the sky," retorted John.

Aeryn looked at him knowingly, "So…you still think something's wrong."

"You know me too well sunshine…yeah my gut still tells me something's off. I mean if they can develop power sources of that magnitude, why can't they clear the skies?"

"Perhaps they do not want the skies cleared," Aeryn suggested.

John's snort was the only answer she got from him.

Aeryn grimaced. "Yeah, I don't like that answer either," conceded Aeryn.

"Whatever the reason we have to get a better in-depth analysis of the situation. We need to send more marauders to check under the clouds and search for any survivors…stealth is out, this time the marauders leave with a full Raptor escort."

"Are you sure that's wise?"

"Maybe…maybe not," he conceded, "I just feel that this is the right decision," he snorted, "At least thats what my gut is telling me."

"Fine, I'll go get the teams ready," Aeryn arched her eyebrow and smiled at him, "_We_ should be able to leave in a matter of arns."

__

Damn, she really did know him, too well in fact.

"Aeryn you're not going anywhere, not in the condition you're in. You could go into labour while on the surface and that would be a problem if we run into any hostiles," ranted John.

Aeryn looked as if she would argue with him. But then suddenly realized that he had a point.

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Perhaps I shouldn't go to Earth's surface;

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At least not on the first trip, she thought slyly.

Aeryn turned and sweetly smiled at him. "Okay I will not come with you."

John looked at her wondering at her sudden change of heart, then it hit, "That's an argument we'll have when I get back," he said as he pointed at her.

**__**

He knew her as well as she knew him.

"What argument?" She replied innocently

He glared at her. "You'll see," he remarked.

She smiled once more at him then left to relay his orders to the marauders.

2 arns later, Docking Bay

The crew was working overtime to get the Admiral's ship ready along with the proper escort. Though the crew were bustling busily there was little sound other than the usual machinery that was in the docking bay. The crew was preoccupied with how events were turning out.

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Especially those concerned with Earth.

Lieutenant Commander Zhann Sun-Crichton was almost finished prepping her marauder to accompany her father to Earth's surface.

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Earth's surface…

When she had been growing up her father had told magnificent stories of all the places he had been. All the places he had grow up in. While growing up, she had loved to hear about her grandfather's cabin in Maine. The greenery there had sounded very relaxing.

__

She had always liked plants, her father said she took after her Delvian namesake, Zhann mused.

The option to just sit and enjoy the scenery on the lake had always delighted her.

Growing up as the Supreme Commander's daughter had not been easy. They had always been wary of assassination and kidnapping attempts all their lives and danger was always prese, now that she was a member of the UMSH military.

But now, she would get to see all the places that her father had talked to her about.

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Or at least the burned out remains of those places…

Lieutenant Sar had returned several arns ago and the rumormill on the ship had been in overdrive ever since he had returned from the preliminary reconnaissance run. When Lieutenant Sar's marauder had docked, he had not even waited for the ramp on his ship to fully deploy. He had ran full-tilt down it and been out of the docking bay heading in the general direction of the bridge before anyone could talk to him.

The rest of the crew had exited the ship more sedately but each one had held a haunted expression on their faces. They had stated what they had found.

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It was something none of us could imagine.

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To find out that Earth was most likely a lifeless moon.

__

It was a blow to all of us.

None of the crew had wanted to believe them. Earth had always held a place in our hearts. They had all imagined it to be some kind of paradise where the good guys always won and the bad guys got what they deserved.

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Discovering that it was even more frelled up than the rest of the galaxy was the mother of shocks!

Zhann shook her head to clear her head of all the depressing thoughts. She had a job to do.

She had to prep her marauder for a trip to Earth's surface.

And her father was scheduled to arrive in the docking bay any microt now.

Luckily, she only had to finish this last review.

Even as she finished, she felt a great silence fall upon the docking bay. Looking up she found her father had entered the bay with his Honor guard of Calcivores.

He walked up to her and said, "Everything ready, Zhanny?"

All his life John had never been able to call his children by anything but the nicknames that they had had as children. Not even with large gatherings of diplomats looking over his shoulder.

Thankfully, Zhann's nickname was not as embarrassing as some of her sibling's names.

"We're ready to go father. All fighters and marauders are prepped and ready for anything," she reported.

"Good, lets get going," John said with a nod. Her father was being very brisk with her, usually he joked before any mission to another planet.

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It was understandable considering everything that was happening.

John walked on to the transport with Zhann in tow. The calcivore honor guard remained behind in the docking bay

A few microts later the marauder and its escorts were underway and heading to Earth.

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Author's Notes: Feedback is appreciated. Again sorry that the last chapter was so short. Ideas of how John should meet Neo and co. are really appreciated. I'm not sure of the timing for the creation of the Matrix. If somebody knows some exact figures, I would really like to know. Also, I suck at coming up with names. Suggestions for names will be really appreciated! Also contact with any of the Matrix characters will not occur for a few more chapters. Sorry. : (


	4. Chapter 3 OH GODPlease No

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What the Hell happened here?!

Disclaimer: I don't own the Matrix or Farscape

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Author's notes: Your reviews were appreciated.

Pete: Thanks for those figures, I've adjusted my timeline accordingly.

Jumper Prime: Great suggestion. I was thinking of doing something along those lines.

Chapter 3 Oh, God… Please NO!

The marauder gently eased into Earth's atmosphere. Zhann Crighton-Sun sat at the controls of the marauder. She kept a close eye on her sensors. This was Earth; anything could happen. Her father was sitting behind her avidly watching everything at once.

"Stand by for some turbulence. We're about to pierce the cloud coverage. Anything may be waiting for us down there," Zhann warned.

Her father's only reaction was to tighten the seat restraints.

The marauder entered the dense layer of clouds. Almost immediately, it began to shake. The shaking got progressively harder and Zhann was forced to fight harder and harder to remain in control.

Suddenly it stopped. They had passed through the cloud coverage.

John worst nightmare materialized right in front of him.

As far as the eye could see, the landscape was a decimated. The burned out hulk of a city dominated John's bird's eye view of his world. The city looked as if it had been massive when it was in its heyday. The buildings were impressively large even by John's considerable standards.

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But they were all in ruins…

It looked like they had been like that for a long time.

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A very long time.

The devastation shocked them all.

For John all his worst nightmares had been confirmed, his civilization was _gone_…

The devastation and destruction was total.

**__**

The ruins looked to be centuries old.

Meaning that the time dilation from the frelling wormhole was even more than John's original estimates. There was no way that all the construction and destruction that surrounded him had occurred in _only two centuries_.

"We're coming up on the city now," deadpanned the copilot.

Viewing the wholesale destruction form even closer was soul chilling. The burned out hulks of building appeared as titanic fossilized skeletons of long dead giants.

John finally brought himself out of the downward spiral his soul had been taking and found his voice, "Where is the nearest energy source?"

Zhann shock of the shock that encompassed her body and checked her sensors, "Its 14000 metras due west from our current position, Admiral."

"Then take there, half speed. Tell our escorts to fan out and look for any signs of life between here and there. I want them to get to know the terrain and look for any intact buildings. I want to what happened Here!!!" Commanded Admiral Crichton.

Zhann relayed his commands and the acknowledgements came in from their escorts. Since John was the Grand Admiral, his escort was larger than normal. It was composed of a half dozen marauders packed with commandos and two squadrons of Raptors.

The Raptors were the latest additions to the UMSH Navy. They had recently replaced the aging prowlers as the main fighters used by the navy. They were significantly smaller, faster and better armed than prowlers but what set them apart from all other fighters was that they were protected by state of the art **Miniature** **Defense Screens**. These had been in development for the past few decades and the ones the Raptors used were the first generation models. The techs were currently trying to develop bigger models for use by larger ships as Marauders but they were having trouble with the increased power output needed by the MDS's for ships larger than prowlers.

"We're coming up on the edge of the area where the emanations are coming form," reported Zhann.

They were leaving the ruined cityscape behind them now. They were coming up on a monolithic structure of immense proportions that stretched out in all directions. It shone with an inner light that was tainted pink. They were a few hundred metras distant from the structure and all that was apparent was lines of metallic gray and silver interrupted by areas of pink in-between.

"I'm picking out lifesigns coming from the structure," reported Zhann with hope in her voice.

"Fine, land next to that structure but keep the rest of the Marauders in air and have the Raptors remain on the look out for anything out of the ordinary," commanded John.

"Aye, Admiral," acknowledged Zhann.

Zhann gently eased the marauder to within a hundred metras of the structure and brought it down gently.

"We've landed Admiral."

"Have zeta squad stand by at the docking ramp. All other commandos are to disburse around the marauder. Tell them to keep their eyes open for anything that moves out there. **You**," John pointed at Zhann, "Stay behind on the ship and keep an eye on your sensors. If anything so much as twitches out, I want to know"

Zhann nodded, managed to keep the disappointment off her face and relayed the orders while John headed down to the landing ramp. Zhann had waited to be with her father when he set foot on Earth.

John met zeta squad at the boarding ramp.

Ever since the formation of the United Multi-Species Hegemony, the military had undergone many changes. The commandos teams used were now of mixed species with special teams for every purpose. Zeta squad was a reconnaissance squad. Recon squads were made of species that were fast, agile and could easily cover various types of terrains quickly. This zeta squad was made up of eight members; three Kalish and five Delvians.

At the boarding ramp, John tentatively took the first step off the marauder and onto Earth's surface.

For the first time in centuries, John Crichton stood on Earth soil. Instead of the fanfare he expected on his return to Earth, he stood on a dead planet that showed only anomalous readings and no sign of normal human habitation as he remembered it.

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I wish that I never went on the Farscape mission, John miserably thought for the first time in nearly a century as he looked around at the ruined landscape all around him.

John shook himself and brought himself back to the present.

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He had matters to attend to.

John and zeta squad headed towards the monolith. A few hundred micots later the reached the structure.

It extended in all directions as far as the eye could see. It was a metallic structure, obviously manmade but John could not see any doors or entryways, **_anywhere_**. About one level up there began row upon row tub-like structures. These 'tubs' had transparent walls and appeared to be filled with a pink substance with a dark shadow at the center, taking up most of space in the 'tub'.

**__**

A humanoid looking shadow.

The butterflies that had been fluttering about his stomach since the first report about Earth turned into irritable ferrets that started gnawing at his stomach wall.

"Looks like we're climbing," John drawled as he looked up at the nearest 'tub'.

"Excuse me sir?" the Delvian squad leader inquired.

"We need to get up there," John pointed at the nearest 'tub', "And I don't see any ladders or stairs nearby. Do you?"

"Perhaps you should let us explore it first, sir?"

"Ah, Ah. No way. Not this time officer. I need to see this through. I need see what's in that pink tub," John looked sternly at the squad leader.

The squad leader nodded in obedience and turned to relay the orders to his men, "The Admiral's climbing this structure. Delvians spread out on the ground and keep an eye on the surroundings. Kalish, spread out in front on the Admiral and look out for any movement. I don't want anything to catch us **_unawares_**!"

Various Aye sirs answered the squad leader.

The Delvians spread out across the ground while the Kalish walked up the wall of the monolith in front of the Admiral forming a defensive arc around John.

They easily made it up to the nearest 'tub' since the wall had many protrusions and was anything but smooth.

John pulled himself up on the edge of the 'tub' and peered into it. The shadow inside was definitely humanoid. At this distance, John could see various cables moving into the 'tub'.

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All of which seemed attached to the shadow somehow or somewhere.

John gently reached out with his hand and eased a finger into the 'tub'. The pink material turned out to bwarm and jelly like.

John grimaced, "This is going to be…gooey."

He gently eased into the tank to stand beside the shadow. He reached down with both hands towards what appeared to be the shadow's head. His hands encountered a hard, fleshy surface he thought was the head. He grabbed a hold and gently eased the head **_up._**

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Up, and towards the surface of the pink goo.

The top of the head appeared first then the rest of it.

**__**

John's heart crystallized.

OH GOD…

Looking up at him was a human visage. The eyes were closed and the head lolled from side in John's grip, but it was definitely a human in this 'tub'. He could see now that the cables were running into the back of the skull through a massive implant at the back of the skull. He could also see a great deal of wires running into all areas of this person's body.

John couldn't catch his breath.

He suddenly let go of the head, stood up, and looked around him.

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AT ALL THE 'TUBS'.

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He realized that they all contained people.

His mind couldn't fathom what he was seeing. Thousands of people, perhaps millions all cocooned in these 'tubs' of pink goo. What could have caused all this to come into existence?

John just stood there trying to understand it all.

Suddenly his com rang out.

Zhann's voice came through, "Admiral we've got movement, **_lots of it_** form all directions. I suggest you return to the ship **IMMEDIATELY**. Please quickly they're moving very fast and will be at location in a matter of microts!!"

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Author's Notes: Hope u like this chapter. Please Read and Review. Sorry it took so long, I had a small case of writer's block. I have little time to write so don't expect any updates anytime soon. Sorry : (


	5. Chapter 4 Encounters

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What the Hell happened here?!

Disclaimer: I don't own the Matrix or Farscape

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Author's notes: Your reviews were appreciated.

SSJ-Mirai-Trunks: Its still there, he's just in shock at the condition Earth is in.

Aaron: Yes the Weapons will work on the Machines, there is no reason for them not to.

Darkvampirewitch: This is set after the first Matrix movie, but I still haven't decided how long after it.

Chapter 3 Encounters

Zhann's voice helped return John to reality. Dealing with an unknown threat was something he deal with automatically, he would not have to think too hard. Which was a good thing since the majority of his brain cells could not get off his discovery of a human in tub of pink goo, wired up like nothing he had ever seen before.

"Admiral…**_DAD_**?! Are you still **_there_**?" An anxious Zhann practically screamed, afraid that something had happened to him.

"Yeah…I'm still here," John gathered his few unobsessed thoughts, "Have you tried talking to them yet?"

Zhann regained her military composure, "I've tried all frequencies even radio. They aren't answering me! They're not in visual range yet but they're coming in on what looks like an attack vector! Please return to the marauder sir, **_NOW_**!" Zhann lost her composure again, her worry over John plainly apparent to John in her tone of voice.

"Keep your shirt on Zhanny, I'll be there in a sec," John replied calmly still to numb to think much. He leapt on to the edge on the 'tub' and started easing down the monolith's walls, all the time dripping with pink goo that made the climb treacherous.

The three Kalish commandos surrounded him and were even more watchful now, scanning the skies for any movement whatsoever with their pulse rifles at the ready. They reached the surface even faster then their original ascent. There the rest of zeta squad reformed around John and they all beat a hasty retreat back to the awaiting marauder. They made it back in record time, the urgency of the situation urging them on the entire way.

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The still barely made it back in time.

The last commando to board the marauder hit the ramp closure button and reported to Zhann, "We're all aboard Commander!"

Zhann's reply came immediately, "**_Then hang onto something!!_**"

Zhann gunned the drive into maximum and with a hefty lurch, launched the marauder into the air.

"Woah there! Easy on the car Zhanny! If you break it I won't buy you a new one!" John sarcastically said as he staggered into the seat behind Zhann.

Zhann rolled her eyes at her father's sarcastic comment, though to her ears he sounded a little strained, "They're almost at our position. What are your orders Admiral?" Zhann inquired seriously.

"Take us up and keep the Raptors between us and them. Let's see what they are going to do," even as John said this he knew that this was going to end badly.

__

I don't intend to start fight today, **this is my first day back Home**, thought John.

"Aye Admiral," Zhann relayed his orders to their escorts.

Microts ticked slowly by as the unkown forces approached.

When they finally appeared on the marauder's sensor screens, John blinked, "You have got to be kidding me…"

The unknown '**_forces_**' heading towards them appeared as a giant mass of wriggling metallic tentacles. Individually these tentacles were attached to round to round silver 'heads' covered in optics that looked like a spider's compound eyes. Each 'head' appeared to have a multitude of wavy tentacles.

****

The attacking 'forces' were giant flying metallic squids.

John snorted at the absurdity and added another absurd moment to the list of absurd moments that he lovingly called his life.

The Raptor squadrons had formed a screen in front of the marauders, which in turn had formed a screen around John's marauder.

John addressed his forces, "DO NOT fire unless fired upon, we don't want a fight today."

The squids came closer and closer and closer.

In hindsight, John realized that he should have known that the squids were not going to stop when they were within twenty metras.

Explosions lit up the stormy sky as squids plowed directly into the Raptor fighter's defense screens. Those that were not destroyed lost tentacles as they tried to attach to the Raptor hulls.

The Raptor squadrons broke formation and spread away at breakneck speeds all the time firing at any squids that came into their sights.

****

Pulse blasts lit up the ruined landscape.

**__**

The majority of their shots missed.

Though the squids did not appear to have the same speed capabilities of the Raptors, they were _definitely_ more maneuverable than _them_.

**__**

Much more.

**__**

They were as maneuverable as the proverbial bat form Hell.

The Raptors continued their deadly dance. But, the sheer numbers of the squids overwhelmed the Raptors' abilities to protect the marauders and more than the marauder's fair share bypassed the Raptors and headed directly for them.

The marauders had already started firing and speeding away from the squids. The majority of squids missed their intended targets.

****

All except a small group attached themselves to one unlucky marauder that had been at the center of the marauder screen.

The com unit on John and Zhann's marauder became active.

"**_WE NEED SOME HELP!!!_**"

"Who is it?" demanded John.

Zhann hastily answered him after checking her sensors, "It marauder six, the squids have attached themselves to their exterior hull."

The com unit continued irrespective of the conversation, "**_These_** **_FRELLING_** **_THINGS are SLICING through the HULL, We've got HULL BREACHES ALL ACROSS THE SHIP!!!!_**" In the background the sound of metal being torn apart was heard accompanied by a continuous symphony of pulse rifle discharges.

Zhann turned towards the embattled marauder. As the it came into view, they could see holes covering the hull surrounded by clusters of squids that were still continuing to cut into the hull as more and more of them slipped into the ship. The marauder was flying straight not maneuvering at all.

Suddenly the marauder pilot's panicked voice filled the speakers of Zhann's marauder, "**_FRELL!!!!!! REACTOR BREECH!!!!!!!!_**"

The ruined terran landscape that had not seen the sun for centuries was lit up by the explosion that looked to observers looked like a small sun.

Before John's eyes had even cleared, he was barking orders into the com unit, "**ALL UNITS RETURN TO THE CARRIER!!!!**"

Zhann propelled her marauder straight up at speeds that pushed her ship's inertial compensators to their limit. John found himself pushed back into his seat and he felt blackness begin to eat away at the periphery of his vision.

Just as suddenly as the maneuver began it stopped.

"Status Report! What's going on?" demanded John.

"We're through the cloud coverage and are leaving the stratosphere, our escorts coming up are behind us," reported a subdued Zhann.

"Good Work," John said but the weight in John's chest did not subside, "Did we lose anybody else?"

"I don't know. We have to wait for them to clear the cloud coverage."

****

Microts passed.

The scanner board beeped.

"We've got another marauder on sensors…a second…four…five, now. Raptors are appearing now, I've got almost twenty three on sensors."

"Who're we missing?"

Zhann checked her sensors, "Omega 7, sir"

John opened a channel to Omega Leader, "This is Crichton. What happened to 7?"

"Admiral…The squids kept crashing into her…her defense screen failed." Omega leader responded evenly, his sorrow audible for all to hear.

"We'll all miss her. We're going to find out who they were and teach them not to mess us soldier."

"Yes sir."

John turned back to Zhann, "Any sign of pursuit?"

"No sir."

"What? They're not coming after us? Why not?" asked John perplexed.

"Uh…I don't know," not sure how she should answer her father's questions.

John thought for a moment, he jumped out of seat, "Contact the Fleet tell them to go to Red Alert! **_NOW_**!!"

Zhann was confused by his orders but never the less immediately relayed his orders.

The Flagship answered her and also delivered some news.

Zhann turned to look at her father and eyed him with some trepidation, "Uh…Captain Sun-Crichton has relayed your orders and requests some clarification. He seeno threats in near by space."

John had been pacing the cockpit but Zhann had stopped him in his tracks. He eyed her warily, "What do you mean **_Captain_** Sun-Crichton? Where's your mother?"

"Uh…she sort of went into labor."

"She WHAT?!" John shrieked.

He sank back down into his chair, his mouth open and closed a couple of times then finally closed it. He sat there looking straight ahead.

Finally he looked up at Zhann and deadpanned, "_And she says I have **bad timing**_."

****

Back Beneath Earth's Cloud Coverage

The Sentinels were swarming under the clouds straining their hover pads, trying to follow the unidentified crafts beyond the lift capacity of their hover pads. They had been significantly reduced in number since the battle with the unknowns.

Beneath them, at the edge of the ruined city, unknown to the Sentinels there floated a hovercraft that had witnessed the battle. Inside sat three bewildered humans wondering what the hell they had just witnessed.

Neo turned to Morpheus and Trinity and asked, "What the hell just happened here? What was all that?"

They just shook their heads and shrugged equally in the dark about who had just been using Sentinels for target practice.

****

Author's Notes: Hope u like this chapter. Please Read and Review.Don't expect an update anytime soon. THIS WAS A FLUKE! I MEAN IT THIS TIME! I've got exams coming up, no time to write. Sorry : (

Question: does anybody know the name for the standard non-FTL drive in the Farscape universe? I can't remember if it was ever mentioned and I've looked for it online but I can't find any references to the name.


	6. Chapter 5 Births and Sensor Logs

****

What the Hell happened here?!

Disclaimer: I don't own the Matrix or Farscape

****

Author's notes: Your reviews were appreciated. I've revised the previous chapters, SSJ-Mirai-Trunks: The answer to your question is in the revised chapter one.

Thanks to everyone that answered my question.

Chapter 4: Births and Sensor logs

The Matrix was in turmoil.

For the first time in centuries, it had been completely defeated by Humans in the real world and an agent had been completely erased from the construct world.

The unknowns had turned out to be humans. They had weapons unlike those seen before and used by the Resistance humans.

The War was going to heat up again…

There were too many variables…

Too many unknowns…

Zhann's marauder came too a complete stop in the docking bay and John was off the ship before she had completely shut down her systems. The docking bay was filled with racing soldiers responding to the red alert, techs prepping Raptors and Marauders for combat and Security officers being dispersed through out the bay.

He raced first to medbay, to check out Aeryn's progress. Once there he found that she was still in first stage of labor and their second youngest daughter, Moya Sun Crichton was there with her, so he raced up to the bridge to see if his fears of an Earth fleet somehow materializing out of thin air had come true or not. His calcivore honor guard was hard put to keep up with him.

The squids had not followed them.

Why?

Was there a fleet somewhere else in the system that was going to come after them now?

He had too know, his fleet's safety depended on it.

The door to the bridge opened and called out, "Jace! Anything on sensors?"

Jason Sun-Crichton, captain of the Flagship, _Farscape 2_, and John and Aeryn's fifth son, turned to his father and said, "Nothing on sensors Admiral, the rest of the fleet reports that can't see anything out here but us," he paused, "Sir, if I may ask what is it you're looking for?"

John nodded, "We were being pursued by some type of flying robots right up until we passed through the cloud coverage. They were very determined to get us and yet nothing came up after us after we passed through the clouds…," he trailed off.

Jason understood immediately, whoever was controlling the squids was prepping their spaceworthy forces, "I understand Admiral," he turned to his sensor chief, "Lieutenant Arnac, keep an eye out for any ships coming up out the cloud coverage," he stiffly ordered.

"Aye captain," the sensor chief said.

__

Now all we have to do is wait for the other shoe to drop, thought John Crichton.

Two arns later, there was still no sign of any Earth space forces and Aeryn was still in the first stage of labor.

The arns had passed by in an eternity with all fleet personnel on edge, waiting for the spaceborne forces to appear, each microt feeling like a lifetime.

Jason approached his father who had been camped out on the bridge, making the bridge crew nervous, "Sir, I don't think we're going to be attacked."

"Jace, we're in Earth orbit, the normal rules of the universe go out the window," John considered the situation, "Fine, stand down to yellow alert. But keep a look out for any strange happenings!" John ordered.

"Yes sir. Stand down to yellow alert, relay the orders to the rest of the fleet," Jason ordered the bridge crew.

John thought about what had to do. Aeryn was okay with just Moya by her side, at least for now.

And he really wanted to check those sensor logs from the reconnaissance mission.

John activated his comm, "Zhanny."

Her reply came nearly instantaneously, "Yes Admiral?"

"Transfer the sensors logs from all the ships that accompanied us to the surface to my ready room and came on up here. We've got some work to do."

Half an arn later, Aeryn commed John, "John," she sweetly called, "If you don't come down here right now," she paused,"…**I'M GOING TO RIP YOUR HEAD OFF!!!**" she screamed.

John visibly winced at Aeryn's tone and Zhann tried to keep from laughing at her father's discomfort, she could hear her sister, Moya, in the background trying to calm their mother down, "Mom, I'm sure he's on his way now…If he knows what's good for his continued survival…" The comm channel closed.

Zhann failed to keep her laughter under wraps and her father turned to stare at her, "Laugh it up Zhanny, just remember this moment when your next assignment comes up," John threatened, trying to get her to stop laughing.

She just laughed harder.

"Fine whatever, just take over for me. Find out who it was we just made an enemy of."

Zhann managed to get her luaghter under control enough to reply, "Aye Admiral."

John turned around and headed for the door muttering to himself, "Well Aeryn's pissed and I've just made us another enemy to add to my list. I wonder how many that makes; a few thousand or was that several thousand?" he shrugged, "Frell if I know, I lost count a few decades ago, or was that a century ago?"

Zhann heard him and smiled, happy he starting to come recover from the shocks that he was currently facing.

A somber John Crichton was not wanted around here.

Bad things tended to happen when he was around.

Zhann returned to analyzing the sensor logs.

Meanwhile down in the medbay Aeryn had finally entered he second stage of labor just as John entered the medbay.

Moya caught sight of him first and frantically waved him over.

Aeryn caught sight of him.

"Hey sunsh…" he started to say.

Aeryn cut him off, "Where the frell have you been?! Did you think this birth was less important than all the others?" she waited for an answer, "WELL?!"

"It's just…"

"It's just WHAT**? SINCE WHEN HAS THE FLEET CAME BEFORE OUR FAMILY?**" demanded Aeryn.

"It's…" John tried to talk.

"**IT'S WHAT?**" cut in Aeryn again.

John sat down next to her bed and said, "Are you going to let me get a word in edgewise or are you just going to continue screaming at me?"

"**_I'm going to continue screaming at you!_**" screamed Aeryn.

"Fine then," said John.

"**FINE**," screamed Aeryn back at him.

Moya and the medical staff just continued about their tasks ignoring their by-play, it happened every time.

Though Moya thought, that this time they were quieter than during her little sister's birth. She had heard their screaming through two bulkheads that time.

Several arns later it was all over, Aeryn, John and Moya sat in the medbay admiring the new additions to the Sun-Crichton Clan; Ashandra and Ashra Sun-Crichton, twin girls.

John was holding Ashandra and Aeryn was holding Ashra when Zhann and Jason walked in on them.

John looked up and said, "Come to say hello to your new sisters have you?"

Jason answered, "Among other things."

John arched his eyebrow, "What happened?"

Zhann answered him, "We found something interesting in the sensors logs."

They walked up to the newborns and stood admiring them.

Zhann continued, "We found some sort of hover craft at the edge of the ruined city…"

Aeryn ears perked up at this, "What ruined city?"

"I'll explain later sunshine, just let Zhanny finish her report," John asked of Aeryn.

Zhann continued, "We were getting human lifesigns from it. There were even humans visible in through their cockpit viewport."

John felt his body begin to tingle, "Were they controlling the squids?"

"No, they were sending out no transmissions, if fact…they appeared to be hiding from the squids. We could scan no visible armaments on their hover craft," Zhann finished her report.

John considered all the information that Zhann's report held with all that he had seen on Earth.

****

One group of humans in pods surrounded by pink goo protected by giant robot squids.

Another group of humans hiding from the squids on an apparently unarmed transport.

WHAT THE HELL IS GOING ON DOWN THERE? thought John Crichton.

He gathered his thoughts and figured out what he needed to do.

He turned to Jason, "I want all stealth prowlers in the fleet prepped and launched. They're to search for this or any similar hover crafts and make contact. They are NOT to engage the squids. At first sign of any squid attack, they're to get their asses back up here. Is that understood Jace?"

"Aye Admiral," Jassaid then left to relay John's commands to the fleet.

"What about me?" asked Zhann.

"You get to stay here with us and take care of your sisters," Aeryn answered, "Your father needs to bring me up to date about everything that happened."

"Sure mom," she took Ashandra away from her father while Moya took Ashra away from Aeryn, "We'll just go introduce them to Serena, she should have finished her studies for toady," Serena was their younger, six year old sister.

They left their parents alone.

"Well what did you find on Earth? And what's this about a ruined city?" Aeryn asked eagerly with concern in her voice.

A little while later Aeryn had heard all that happened to John on Earth and was as confused as he was, "I expected things to be weird but this a bit much, even with the twists our lives usually take."

"I know…You know what's really bothering me now?"

"We won't know anything until they make contact."

Aeryn nodded, agreeing with John.

****

The waiting was always hardest on them.

****

Author's Notes: Hope u like this chapter. Please Read and Review.

****

Next time: contact with the Resistance.


	7. Chapter 6 Needle in a Haystack

****

What the Hell happened here!

**Disclaimer: **I don't own the Matrix or Farscape

**Author's notes: **Your reviews were appreciated. Sorry for the delay some writer's block combined with exams are responsible, not me! Thankfully I am now finished! I've got three weeks rest and I intend to make some progress in this and my other stories, so expect rapid updates : )

**Gatemaster**: thanks for pointing that out, it's fixed now.

**SSJ-Mirai-Trunks**: could you explain what you mean by 'its hard enough'?

Chapter 5: Needle in a Haystack

The fleet sent out numerous squadrons of stealth prowlers to search for the second group of humans. In the mean time the fleet had spread out across the Sol system looking for any signs of human habitation.

The Hegemony Fleet that John had brought with him was composed of ten vessels. There were two _Vigilance_-class frigates along with a pair of male Leviathan gunships, Danok and Tarsos respectively. Accompanying them were three _Prometheus_-class light cruisers. These were multi-purpose vessels that had come into service at the birth of the UMSH and were considered the most versatile support ships in the Fleets.

The Fleet was rounded out by the presence of three major heavy cruisers. A _Sundance_-class Command Carrier, by the name of _Far Horizons_ and captained by a female Delvian called Cassifa. This was the first class of Command Carriers built after the formation of the Hegemony. It was one and a half times the size of the old Peacekeeper Carriers with almost double the weaponry in addition to heavier armor and a significantly stronger defense screen.

The second cruiser was a female Leviathan cruiser called Jalina. She was the oldest Leviathan hybrid serving the Hegemony Navy and was the second armed Leviathan born from Moya. And she was the single most temperamental female Leviathan in existence with a viscous streak of legendary proportions. Half the time she uncontrollable especially if her friends or children were in danger. She would have been removed from active service in the Hegemony Navy if not for her latest pilot who had finally proved himself capable of controlling her, for most of the time…  
Her captain was none other than another of John and Aeryn's offspring; Ben Sun-Crichton.

The final cruiser was John Crichton's flagship, a modified _Talyn II_-class Command Carrier, the _Farscape II_, under the command of Captain Jason Sun-Crichton. This Command Carrier was the largest and most powerful warship in the fleet, reaching 5000 metras in length with an arsenal of weapons unmatched by any other vessel in the quadrant.

Each of the three cruisers took a geosynchronos orbit around Earth will the other vessels of the fleet were charged with combing the Sol system for any unusual activity. The cruisers were constantly scanning the clouds searching for a way with sensors to breach the sensor opaque barrier surrounding the planet. They were especially on the lookout for any ships penetrating the cloud coverage.

One month later they were still looking for the second group of humans and all their extraplanetary searches had turned up empty.

To say that this was frustrating for John was to say that Scarrens are only slightly viscous.

The only good thing he could see coming out of this mess was the amount of free time he had to spend with his new born twin daughters. This took up the majority of his time.

The rest was the time he spent getting on his subordinate's nerves and running surprise drills and inspections.

The stealth prowlers surveying Earth's surface had extensively searched through the ruined city and other's like it.

These searches had turned up nothing.

Until one day an alert pilot had discovered something that made John want to repeatedly bang his head against the wall.

Something that had illustrated to John very clearly just how big of a haystack he was searching in.

The pilot had found a tunnel leading to an underground multilayered plexus of tunnels and caverns that ran for kilometers in all directions, undermining the entire continent.

It was something that caused a great deal of headaches at John's weekly senior captains meeting. The meeting was being held on the _Farscape_ _II. _Three captains were present; Cassifa, Ben Sun-Crichton and Jason Sun-Crichton.

"Do we have any idea how large an area we have to search through?" asked John, he feel a headache beginning behind his temple.

The three captains looked helplessly among themselves and then Jason said, "Well, uh…not really sir."

John moved over to desk and sat down, "…why not_?" This was going to be a very long meeting_, thought John.

"Well sir it's just that the tunnels are a virtual labyrinth that twist in on themselves, double back or come to unexpected dead ends. It's impossible to know how much of an area there is down there," Jason paused for a moment in his explanation, "And there have been **_complications._**"

The pain in John's head blossomed into a full-blown migraine, "What complications?" John asked knowing full well that he did not want to know.

Jason answered him quickly; "Some of our prowlers have encountered more squids. They were patrolling some of the tunnels. Thankfully we didn't have any casualties. The squids visual sensors managed to pick out the prowlers easily but when out of visual range they easily missed spotting our fighters."

John started rubbing his temples as his migraine intensified.

_Why does Murphy love me so?_ thought John sarcastically.

To his captains he said, "So basically we have a labyrinth with no Theseus in sight?"

His captains did not answer him.

John slowly nodded his head, "I'll take that as a yes," John sighed, "Do any of you have any recommendations? Suggestions? Hare brained ideas?" asked John sarcastically.

The three captains exchanged glances then Cassifa spoke up, "Well I do Admiral…"

"Well little girl speak up, I'm not getting any younger here," drawled John.

Cassifa hid her amusement; it had been several centuries since anyone called her a little girl. "Well sir, perhaps we need to create a commotion, something to attract the squids. The second group of humans may investigate what is attracting the squids's attention," Cassifa finished.

John scrutinized her for a few microts, then said, "That's actually a good idea," he turned to look at his two sons, "Didn't I tech you boys to come up with plans before everybody around you?" he sarcastically inquired.

They just rolled their eyes at his needling.

John thought more on what Cassifa's suggestion would entail, "Since this is your idea, what kind of diversion did you have in mind?" He asked Cassifa.

"Well," she began, "The Human ship was attracted to our skirmish with the squids. Perhaps if we stage another skirmish they would appear," she theorized.

John thought on her idea. It had merit but he did not want to recklessly endanger any of his troops. He mentioned this to her.

"It was merely one possible solution," she said with a shrug.

"It could still work," mused Ben, "All we have to do is use a bigger ship. I doubt they would have enough firepower to break through a Leviathan gunship's defense screen," he explained.

Jason looked at his bother pointedly, "So let me get this straight, you want Danok and Tarsos to become targets and play tag with the squids?"

"Well I was thinking Jalina and I would be doing the flyby but your way could work as well," said Ben innocently.

Jason glared at Ben, "And if she gets antsy and fires back with her main weapon? What if she hits one of the monoliths? Does she **_accidentally_** kill a few **_thousand_** humans?"

"She won't."

"I've heard that before!" retorted Jason.

The two siblings glared at each other.

"_Boys_…play nice," John teased, he turned serious, "I'll take it all into consideration and get back to you all."

The three captains recognized John's curt dismissal of them and saluted smartly, "Aye Admiral," they all said then left the admiral's ready room, Ben and Jason jostling each other along the way and Cassifa shaking her head at their childish antics.

Neo lay in his bunk on the Neb. Trinity was curled up next to him using his arm as an extra pillow. He was supto be sleeping but his thoughts were too complicated. Ever since the Sentinels were fought to a stand still by an unknown force, a month ago, the war had gotten more dangerous.

A week after the battle, another resistance hovercraft had encountered a new type of Sentinel.

****

One armed with a projectile energy weapon.

The hovercraft had barely escaped, and not without. Also Sentinel patrols in the tunnels had increased almost fivefold, forcing the Neb to spend most of its time in hiding, unable to do anything.

What little time they had had left, was spent in a trip to Xion, the last free human city.

They had gone there to repair the damage the Neb had received during Neo's battle with Agent Smith. They had also taken on new crew to replace the ones that had been killed by the traitor Cypher.

Neo had expected Xion to be many things…**_except what he found_**.

The defense there had been formidable and the Mainframe controlling it all there had been beyond his imagination, but…

****

Everything else was abysmal.

The conditions there were worse than those he had seen on CNN and the Discovery Channel depicting the poorest third-world countries.

The people of Xion were surviving but not living.

They ate the same slop that was on the Neb. Medicines were in high demand and short supply. Communicable diseases as cholera and influenza ran rampant though the population. There were no animals, only a few types of insects and the only abundant plant life was a weird type of sulfur smelling fungus that was everywhere.

And there was 5 million humans squashed into an area meant only for a few hundred thousand…

And there was no hope in sight…

****

Except him.

It was **_all_** riding on him now.

The **_only_** hope for 5 million humans.

****

The last free humans of Earth.

The responsibility was overwhelming him.

****

How was one man supposed to change things?

How was he supposed to save humanity?

The Oracle had said he was not the One. How was he supposed to tell them that?

Sudden banging on his door broke through his sullen introspective mood. The door burst open and Kat one of the new crewmembers shouted, "Neo! Trinity! Wake up! We've got major Sentinel activity!"

Trinity woke with a start while Neo said, "What's happening?"

"Every Sentinel in scanning range is heading up to the surface, fast!" Kat replied breathlessly, "Come on!" she urged them, she ran from the room.

They quickly followed her to the bridge. They found Morpheus already there sitting at the controls stealthily following the rearmost Sentinels up to the surface.

"What's happening?" asked Trinity as she took the copilot's seat next to Morpheus

"I don't know. I've never seen this much Sentinel activity. Ever!" answered an uncertain Morpheus.

They slowly followed the Sentinels in silence, all of them wondering what could possibly cause such unusual behavior in the Sentinels. They had many different suspicions but one was common between them:

The interlopers. The unknown group that had engaged the Sentinels were somehow involved.

When the reached the surface they found the sky blotted out by masses of Sentinels, thousands strong.

But that wasn't what shocked them.

The Sentinels were attacked two fast moving ships larger than the Neb, that were moving at supersonic speeds and pulling off maneuvers that a hovercraft could never do. Even as they watched a third ship passed between the other two and the Sentinels.

But the third ship was gigantic! It looked large enough to swallow the Neb whole and still have room for several more hovercrafts. The sensors said that it was over two klicks long! And it was moving at supersonic speeds!

Neo found his voice first, "Oh my God! What are those things!"

**Author's Notes: **Hope u like this chapter. Just a little cliffhanger to keep you on the edge of your seats. Please Read and Review. First contact should occur in the next chapter.


	8. Chapter 7 Contact

****

What the Hell happened here!

**Disclaimer: **I don't own the Matrix or Farscape

**Author's notes: **Your reviews were appreciated.

**Alatoic01:** The other two movies will NOT occur, I watched them and didn't like them so from this point on I'm making everything up as I go along. As for the Animatrix well I haven't seen it, if I do I might or might not use or reference it. Also John is not the same hothead that he was in the series, he's more mature (mainly but not always) so he wouldn't attempt something like that without prior preparation and good cause.

**Janusi:** They will get most of them but not all. The Matrix is constructed around the 20th century, not an exact duplicate.

**Darklight**: ...? What are you psychic or something? How'd you know I was going to do that?

Chapter 6: Contact

In the arns that followed the senior captains meeting, the three captains, Ben, Jason and Cassifa had hammered out a workable plan out of Cassifa's original idea. It had not taken very long and John had approved it in even less time.

So there they were the three Leviathans in the fleet; Jalina, Tarsos and Danok, on final approach to Earth. They were going to trigger a reaction from the squids in the hope that that this would cause the second group of humans to show themselves. When they appeared the Leviathans were supposed to try and make peaceful contact with them.

Hopefully then someone could explain what the hell was going on Earth!

Ben Sun-Crichton stood on Command in Jalina. He felt her discomfort at entering the atmosphere of such a dead planet. She also worried for her two children's part in this plan, their defense screens were not as powerful as hers.

Ben could feel what she was thinking of doing if the squids hurt them.

Ahead, the two gunships passed through the cloud cover first. Jalina hovered just above it, the plan was for her to wait a few hundred microts before following her children in.

The microts passed as arns.

When they were finally over Jalina rapidly accelerated forward, following her children through the clouds.

They rapidly passed through the clouds. The situation they found below was **_almost_** as they had predicted it to be.

Almost but not quite.

The squids engaging the two gunships were more numerous than had imagined they would be, but what concerned Ben was that some of them appeared to be armed with some sort of laser weapon. These squids were firing at the two evading gunships at an impressive rate. Ben checked his sensors they also packed an impressive punch for something that small. The gunships weren't firing as per their orders.

Ben felt Jalina's concern blossom into full-blown rage. He felt her begin to charge her main weapon intending to blast the squids into oblivion.

_Oh frell_… thought Ben.

"Jalina NO!" Ben shouted, "NO FIRING!" he commanded adamantly.

He fought with her control telling her to just fly in between the squids and her children. They could not afford any collateral damage, the backdrop of the squids was a monolith.

Jalina continued to accelerate towards the engagement.

She swooped in at supersonic speeds through the squids' formation.

The squids' formation was scattered in her wake. Many of them flew into their brethren while others crashed into Jalina's defense screen. What cohesion they had had was completely lost. Even more were scattered by her wake trail.

While the squids were reacting to this new threat, the two gunships shot across to Jalina status reports; the squids had appeared as they flew over the monolith and their defense screens were holding but there was still no sign of the human hovercraft.

_Fine_, thought Ben, _then we provoke them more…_

Ben opened a comm channel to the two gunships, "Open fire, one quarter power only!"

The dark lit up with weapons fire form the leviathan gunships. Jalina did not open fire.

This threw the squids into even more chaos than they were already in.

Squids began disappearing at an alarming rate and explosions filled the skies.

The engagement drifted away from above the monolith till the ruined cityscape was underneath.

The defense screen on one of the gunships began to weaken and Jalina began to get antsy and ready to fire. Ben ordered that one to withdraw to their rally point above the clouds. The captain protested but followed Ben's command. The gunship; Tarsos reared up on its end and shot straight up at maximum speed. It was out of sight in a mater of microts.

Ben was starting to become concerned. At the rate they had been destroying squids they should have destroyed them already, they were being reinforced, but from where? "Jalina were are they coming from?"

Jalina checked her sensors and pointed out that they were coming from underground the ruined city.

Ben decided that when he got back he would have to have the mapping of the tunnels prioritized. They had to know what was hidden down there.

Jalina screamed for his attention, "What is it?"

He checked the scanners and found what she was screaming about.

The Human Hovercraft!

It had been hiding in a building covertly watching the battle but Danok had accidentally hit most of the rubble hiding it from view and now it was rising into the air. Half the squids engaging the Hegemony Leviathans had broken off from the engagement and were heading in its direction, the squids equipped with lasers were already taking ranging shots at it.

_So that rules out them controlling the squids_, thought Ben.

As he watched the hovercraft he so desperately needed to contact turn tail and run as being pursed by a pack of starved calvivores, with a couple of thousand squids on it's tail.

A desperate solution to this conundrum came to him.

One that was reminiscent of some of his father's more insane and colorful plans.

"Jalina, after that hovercraft! Maximum speed!" commanded Ben.

Jalina turned towards the hovercraft. She rapidly gained on the squids pursuing the hovercraft, opening fire with her smaller anti-fighter plasma canons as she passed them.

She bypassed the now disorganized group of squids and continued to accelerate towards the fleeing hovercraft.

She reached it in short order, "Jalina, activate the docking web! Drag them into your docking bay! Before the squids reach us!" shouted Ben in excitement.

The hovercraft was unceremoniously dragged into Jalina's bay. Once it was completely inside the docking bay, Ben gave the retreat order and the Hegemony forces left Earth's surface. Their mission accomplished.

****

Technically speaking.

XOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXO

The crew of the Neb were passing out weapons, trying to grasp the situation they were now in.

One minute they had hiding behind some fallen debris watching in awe as the interlopers totally overran the Sentinels, shrugging off all attacks aimed their way, safe under some sort of energy shield, the next the had been fleeing more Sentinels they had all seen in their lives. The minute after that they had been run down by the largest ship and dragged inside by some type of tractor beam.

They hanger they found themselves in was reminiscent of things they had seen in SCI-fi shows. They had seen the same viscous looking fighters that had engaged the Sentinels that first time. But was also been other ships there, another type of organic looking fighter and larger organic looking transports. They had even caught glances at small round things that seemed to flow across the floor at rapid speeds.

****

Whoever these people were they were definitely not from Kansas.

They did not know what to expect…sure the interlopers had fought the squids, but why? What were they trying to accomplish? What were their intentions? Perhaps they were going to destroy the machines? Perhaps they were going to destroy the machines then enslave humanity for their own purposes?

All these thoughts and more were running through the crews' minds.

Suddenly Trinity screamed out from the cockpit, "Morpheus! Neo! Get up here, NOW!" there was almost a hysterical edge to her voice.

Morpheus and Neo exchanged looks, then Neo grabbed a weapon for Trinity and they headed for the bridge.

They found her staring, in open-mouthed shock, out the viewport at something outsithe Neb.

"What is it Trinity?" asked Morpheus in a concerned voice.

Wordlessly she raised a shaking hand and pointed out of the viewport at something.

Neo and Morpheus followed her finger to where it was pointing.

They gasped in surprise, it was if they had been physically struck.

Standing at the foot of the Neb directly in front of the viewport was a man.

****

A human man.

He was attractive, tall with long shoulder-length blonde hair held in a ponytail and an average build. He was wearing a green and black uniform with some sort of patch on his chest.

And he was slowly gesturing with his hand, inviting them to join him outside the Neb. He smiled sheepishly then held up his right hand in an age-old gesture that they all recognized.

"Isn't that that thing that Spock does on star trek?" asked a stupified Neo.

Nobody answered him.

The man gestured again at them, while smiling encouragingly.

Neo looked at Trinity and Morpheus the shock still hadn't filtered through their systems, "Well are we just going to sit here?"

After a while, Morpheus finally seemed to come out of his shock, "No. We're going down to talk to him. All of us," he decided. He was preoccupied with what this could mean. Had other humans survived? Were they ready to take on the machines and take back what was rightfully theirs? Or was this some type of trap by the machines?

Morpheus didn't know.

The three of them left the cockpit and went to get the rest of crew.

They found Kat, Tank and Fio waiting for them by the weapons cabinet.

They all saw the disbelief on their leader's face, "What is it?" asked Tank.

Trinity answered him, "You won't believe it without seeing it."

Morpheus gestured for them to follow him.

Kat, Tank and Fio exchanged bewildered looks but nevertheless followed Morpheus to the exterior hatch. Morpheus opened the hatch and he stepped out into the unknown ship's hanger. The rest of the crew followed him.

They walked a few paces away from the Neb before they encountered the man. Kat, Tank and Fio's mouths dropped in surprise when they saw him and Neo could now see that he had blue eyes top match his blonde hair.

Muscles rippled under his uniform as he raised both his hands with palms open to show that he meant no harm as he slowly approached the crew of the Neb. He stopped 3 meters away dorm them.

The two groups stood staring at each other, examining each other. The frowned in confusion when he saw some of the crew's implants but quickly replaced it with another smile. Kat, Tank and Fio were still trying to assimilate this totally unexpected development.

The man spoke up first, he spoke in slightly accented English, "I come in peace. Take me to your leader."

Surprise blossomed once more as the unknown man quoted yet another famous Earth saying and Morpheus hesitantly stepped forward and looked the man in the eye, "Who are you?"

The man smiled and opened his mouth to speak; "I am Captain Ben Sun-Crichton of the United **_Multi-Species_** Hegemony Leviathan Hybrid Heavy Cruiser, Jalina." He paused for a second, "And you are?"

Their jaws dropped again.

****

This they definitely had not expected.

**Author's Notes: **Hope u like this chapter. Please Read and Review.


	9. Chapter 8 Introductions and Preliminary ...

****

What the Hell happened here!

**Disclaimer: **I don't own the Matrix or Farscape

**Author's notes: **Your reviews were appreciated. Wow I've never had that many reviews for one chapter before ! Thanks!

**RavynJensen: **Why?

**Dr Shubert: **Just like in the movies the second law of thermodynamics is being ignored. Of course, its possible that the machines have discovered some new law that we do not know of. ;)

**grayangle: **This is not going to be a dead story unless something happens to me, I've already planned out the middle and end of it and baring any unforeseen circumstances will be finished. But new chapters will not be finished quickly because university takes the majority of my time.

**Darklight: **First part of your prediction is right, the rest, well I don't know yet.

**Chapter 7 Introductions and Preliminary explanations**

**"_You're who?_" **exclaimed an incredulous Neo.

Ben took a deep breath knowing that this was going to be a very long conversation, "I am Captain Ben Sun-Crichton of the United Multi-Species Hegemony Hybrid Leviathan cruiser, Jalina."

"Oh, that's what I thought you said…" Neo turned to look at the other humans, "He's a captain in the United Multi-Species Hegemony…" the crew of the Neb looked dumbly at Neo, they were still in shock after Ben's introduction. He turned back to Ben, "That's a hell of a name you got their."

Ben smiled at the Neo, "Now that I've introduced myself could you introduce yourselves?" he asked innocently.

Morpheus managed to regain his voice, he stepped forward, "That is Neo, that is Trinity, Tank, Kat, Fio and I am Morpheus, leader of the Human Resistance," he said pointing to each person as he said their name.

"Resistance? Against who exactly?" the excitement was building up inside of him, finally some questions were going to be answered.

"Against the machines of course, everybody knows this," said Trinity in confusion, "How can you not know that? Everybody human does…" she trailed off as she logically followed her comment to the end.

Silence descended on the humans again as the realized that the human they were standing with was not a human.

Ben smiled nonchalantly at them.

Morpheus slowly spoke up, "You're not human," it wasn't a question.

"Well not entirely," Ben truthfully answered, "I'm only half human." The answer to his question registered, "Machines? Who's controlling these machines?"

"No one. They control themselves," answered Morpheus gravelly, "Wait a minute…You're half human! What's the other half?"

Ben smiled depreciatingly, "I'm also half-sebacean."

They looked amongst themselves and then Neo asked dumbly, "What's a Sebacean?"

Ben took a deep breath knowing that this was going to elicit a reaction, "Basically, I'm a human/alien hybrid."

For a moment there they collectively looked as if somebody had sucker punched them.

"But…But, you look human," protested Kat.

Ben turned around and gestured behind him. A few seconds later an attractive curvy blue eyed blonde human woman wearing the same type of form-fitting uniform as Ben walked up to them.

"This is my second-in-command, Commander Iliana…and she's not Human, she's a Sebacean," explained Ben.

Their eyes became as wide as saucers in surprise.

"…Sebaceans are visually indistinguishable from humans," continued Ben. He paused and looked at the Humans waiting for them to recover a little from their shock.

The mind of each of the humans was reeling with each successive revelation.

"Are…are all aliens so human-like?" asked Trinity, still in disbelief of all that was being revealed.

"Ah, no. Though most Hegemony species are humanoid, except for a few notable exceptions, like the Hynerians. My father likens them to Kermit the frog, that should give you an idea of what they look like," answered Ben.

"**_There's an alien species that look like Kermit the Frog!_**" exclaimed Neo, this was simply to much to imagine.

"That's what my father says," Ben said with a shrug.

Morpheus felt hope blossom in his body as an idea came to him, "Does this mean there is a free colony of humans among this Hegemony?" he said excitedly. This could provide more hope for the people of Xion than they had ever had.

The others perked up as they realized the same thing that Morpheus had.

Ben grimaced, "Unfortunately, no…"

****

The hope died in the humans with those two words.

"…My father is the only human in the Hegemony," finished Ben.

"But who is your father?" asked Trinity inquisitively.

"My father is the former IASA astronaut, Commander John Robert Crichton Junior and current Grand Admiral of the Hegemony armed Forces," proclaimed Ben proudly.

"How the hell did he do that?…IASA? Don't you mean NASA?…There hasn't been an Earth space program for over a century!" demanded Neo.

Ben looked at Neo strangely after his outburst and said, "That is a very long story, one I do not have enough time to tell. NASA was a part of IASA, and further more, are you sure it's only been a century?"

Neo opened his mouth to answer then stopped, _was he sure?_

The answer was neither, he nor Morpheus nor anybody in Xion was sure of the exact date.

"Uh…no," replied Neo lamely.

Trinity asked insistently, "But how did he come to meet Aliens?"

"Basically he was accidentally shot through Earth's latent wormhole and landed in the far side of the galaxy during a mission, that was about, oh…a hundred cycl-years ago, by his reckoning," answered Ben.

"Then he's not going to be able to explain all this," said Neo, stating the obvious, John Crichton would be long dead by now, thought Neo.

"Uh…" this was about to get tricky, thought Ben, "Actually…he's waiting for my report on his flagship."

"What? Didn't you just say that he left Earth 100 years ago? How can he still be alive?" demanded Neo.

"Well, that's easy to explain. He's had a little genetic modification," Ben said while bracing himself for the coming outburst.

They did not disappoint. "**_He's had what!_**" they screamed at him, "Willingly?" asked Neo in disbelief.

"Actually…No, not willingly, its a long story," Ben gave a dismissive wave to signify that they should not ask for more details.

The humans all stood in silence contemplating all they had just been told.

"So basically, what you're telling us is that you are a part of a Hegemony that is comprised of multiple species. The ship we're on is a one your cruisers and you're taking us to meet 100+ year old human who should be dead but instead has mated with an alien and is the commander of the armed the forces of the Hegemony?" Neo summarized.

Ben cocked his head as he thought for a moment then said, "Yeah, basically."

"You actually expect us to believe this incredible story?" asked an incredulous Trinity.

"Of course not…not without proof anyway," said Ben simply. He gestured once more behind him.

Sharp gasps of surprise from the humans heralded the arrival of more aliens.

This time there was no doubt in their minds.

They had wanted proof and now they had it. Standing before them were three figures, who were anything but human. All three of them were large hulking creatures. The smallest of the figures was humanoid but with an elongated chin and tentacles coming out of his massive dome-shaped head. The next largest was reptilian to the extreme with a long thick neck that sprouted out of its shoulders so that its head was a couple of paces in front of its body. It was covered in gray scales. The last of the trio was the most massive. He stood a full head taller than the reptilian. He had pale humanoid face but there was some type of headdress attached to his head with weird bulbs at the sides and directly above. The last one gave them a nice toothy smile with lots of short sharp teeth.

Neo leaned close to Trinity and quietly whispered, "Are you sure we're not still hooked into the Matrix and we don't know?"

Trinity did not look at him but whispered back, "We're not still hooked up to the Matrix."

The humans now stood staring at the aliens, knowing now that Ben had been telling them the truth.

Ben smirked at them, "Let me introduce three of my subordinates," he pointed to tentacles, "This is Lieutenat Zi Gandral, he's a Luxan" he gestured to the lizardman, "This is Officer Kwaen and she's a Scarren." He nodded his head at the final alien, "finally we have my head of security, Sub-commander Lee'Tam, he's a calcivore."

Ben looked at the humans and decided it would be best to wait until they absorbed these latest shocks before springing anything else on them. He dismissed his officers and his 2IC with a curt gesture.

They left the docking bay leaving Ben once more alone with the humans.

The crew of the Neb all stood in silence for a long time all of them trying to get to grip with the aliens they had just seen and the half-breed that was standing with them.

"Wha…What are you…your intentions?" asked Morpheus after much deliberation, and even though he had not yet managed to assimilate all the information that had been laid bare in front of them by Ben.

"We only wish to open diplomatic relations with Earth and its peoples," stated Ben.

"But why now? Why not earlier?" Morpheus questioned insistently.

"Because it's taken us this long just to find Earth. It took us six months just to get here from Hegemony territory after we pinpointed Earth's location," explained Ben simply.

"Oh…" said Morpheus lamely.

Morpheus looked around at the rest of his crew. Trinity and Neo were clutching each other's hand, trying to come to terms with that been said. Tank was starting to look shell-shocked. Fio and Kat looked to be quietly debating something between themselves.

"…We are currently heading for our flagship, the Farscape 2. Their you can meet Grand Admiral Crichton, we'll be there in short while," Ben paused, "I need to update the admiral, so I'm going to leave you alone. If you require anything or have anymore questions than just call out for me. Either myself or Iliana will came," with that Ben nodded and started to walk away from the humans.

"Okay…" muttered Morpheus, "Everybody back into the Neb, we need to talk," he commanded.

XOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXOXO

Ben walked into the corridor leading away from the docking bay. He found his wife, Commander Iliana Sun-Crichton waiting for him there.

"Well?" she asked.

"They didn't take a shot at me…I'll take that as a good thing," remarked Ben.

She scowled at him, "I know that, I meant did you find out what the frell happened to Earth? Why is it lifeless?"

"No, though they did mention something about fighting machines. The one called Morpheus said he was the leader of some sort of human resistance. I didn't press them. Let them first come to terms with all I've told them…dad'll get what happened from them later," Ben said irritably, "But first I have to tell him what I did."

Iliana winced, "You still haven't told him, yet?" She sighed.

Ben looked at her sheepishly, "Well I have been a little busy explaining everything to our new guests. I was going to call him now."

"This I have got to hear…" commented Iliana.

Ben glared at her and activated his comm, "Admiral Crichton."

His answer came quickly, "Crichton here, Benjie that was fast, have you made contact?"

"Definitely sir," Ben said wholeheartedly. Iliana raised her eyebrows at this remark.

"Excellent. Any trouble with the squids?"

"Not much sir, though we did encounter a new model, it'll be in my full report," Ben added hastily.

"Fine as long as everybody's all right. Did Jalina blast anybody into oblivion today?" John Crichton asked innocently.

"No sir, only the squids were damaged in any way. The monolith is intact," Ben managed to reply with a straight face, while Iliana rolled her eyes at him.

"Good work. What did the Humans have to say, when you talked to them?" queried John.

"You can ask them yourself when we dock," Ben braced himself for his father's reaction.

"…………_What do you mean I can ask them?_" asked John quietly, while Ben winced at his tone.

"Well…its just that during our engagement and their hovercraft appeared and came under attack by the squids. They were about to be destroyed, so…so I had to intervene," just a few more moments and his father's wrath would be upon him.

"Intervene how?"

Here it came, "I, well…I was forced to do something drastic sir."

"Drastic? Drastic you say? Just how drastic?" asked John, his tone the personification of innocence.

Ben gathered up what little courage he had left, "Yes sir, I was inspired by your past accomplishments; I had Jalina drag the hovercraft into her bay with her the docking web."

He heard his mother's laughter in the background, "Not a word Aeryn, not a single word!……**_WHAT THE FRELL WERE YOU THINKING!_**" John screamed at him, "**_What the dren were you trying to accomplish?_** Now they're going to be extremely hostile towards us!" John ranted.

Iliana grinned at her husband and he glared daggers at her.

"Actually sir they appeared quite reasonable when I talked to them," added Ben quickly before his father could continue.

"You talked to them after you took them onboard! Damn, Jace was right nothing goes as planned whenever you and Jalina are involved," the last part was muttered under John's breath. Laughter came over the comm.

"It's not funny Aeryn!" denied John in an indignitly.

"Yes it is! It what you always call…Kama," came Aeryn's retort.

"It's Karma and no it isn't!" John denied vehemently, "anyway that's not the point! Ben how long until you reach us?"

"It should be in another 40 microts, sir" answered Ben while trying not to laugh at his parents' antics.

"Good. Dock with my Command Carrier and I'll be there as soon as I can," the comm link closed.

"Well that went well," said Iliana sweetly to her husband as she smiled coyly.

He turned to look at her and gave her his iciest stare that had absolutely no effect on Iliana.

She just continued to smile coyly at him.

**Author's Notes: **Hope u like this chapter. Please Read and Review.


	10. Chapter 9 Introspection

****

What the Hell happened here!

Disclaimer: I don't own the Matrix or Farscape

****

Author's notes: Your reviews were appreciated. Thanks!

Alltorian: Hopefully this chapter will explain everything.

Darklight: No the Agents are not working on spaceships and Crichton will meet the Matrix crew in the next chapter. Oh and when Crichton finds out about the fate of humanity he will not take it lying down…and that's all I'm going to say for now!

Mirth513: Thanks for that review it really made my day when I read it:)

Chapter 8 Introspection

Aeryn Sun sup up in her bed as she nursed one of her newly born twins. Her mind was not paying attention to the task at hand. Too many other things were plaguing her consciousness.

The long years were wearing heavily on her mind. They had passed so quickly and so many changes had happened then should have been possible…

She could remember how it all stated as if it was yesterday…It was supposed to be a simple mission, escort a convoy of prisoners to a penal colony but one leviathan had broken free. She had been firing on it as it had Starburst…

Aeryn shook her head…She'd met John that eventful day. She thought about all that had happened afterwards, they'd been hunted all across the Uncharted Territories and Tormented Space for 4 years before war had broken out with between the Peacekeepers and the Scarrens.

__

They'd lost Dargo then.

And John had lost the wormhole tech in his head along with Harvey after forcing peace onto both warring factions with the help of the Eidolons.

She and John had thought they could have lived out the rest of their lives in peace with their newborn son…_they were proven so wrong._

The Nebari had attacked…everyone!

Countless worlds had quickly fallen, the Scarrens and Peacekeepers had been incapable of stopping the onslaught of Nebari forces. The Nebari plague had pacified worlds before any resistance could form. And the Eidolons…their powers had proved useless against the Nebari. The mindcleansing technology they employed had become a wall against the persuasive powers of the fabled Eidolons.

Moya had fled from one world to another searching for a peaceful place to hide, but none had been found.

Eventually they had found themselves at the Royal Planet, where the world of Aeryn Sun-Crichton was once again turned on its head as Fate once more changed Aeryn's position in the universe. Empress Novia, along with representatives of all the major and remaining powers had given John an offer he could not refuse…

They would hand **HIM**, John Crichton of Earth, command of a their remaining forces. **HE** was the only one they would all trust not to misuse all the power that came with this position.

So he had taken command and she had been there to support him through it. Every nerve wracking moment of it.

"Ouch." Aeryn cried out as her new daughter bit down hard on her nipple. She gently repositioned her daughter and began paying more attention to her daughter's care. She was going to be back on duty in a few days she should just her enjoy this quiet time.

Elsewhere on the ship, John Crichton strode briskly down the corridor of his flagship pondering what the hell to do with Ben; he was just too much like his old man.

Truth be told he had done exactly what was required of him, he'd been sent to make contact with the second group of humans…and he had.

Just not in the way John had expected…**_then again since when have the Sun-Crichton family done anything in the normal and expected way._**

Anyway, all these thoughts were running around his mind trying to distract him from his upcoming contact with the humans.

**__**

Humans!

It had been a century since he had talked to another member of his species.

Would they remember him? Would they revile him? Would they be able to tell him what the hell happened here?

There were so many questions unanswered and he wasn't going to get any of them answered till he reached the conference room where Ben and Iliana were waiting for him.

Add to that, Aeryn was still too busy with the twins to oversee the fleet, so Jason was to do her job. He was good but Aeryn and John simply worked together better. She always knew what he would order before he opened his mouth.

John blew out a sigh.

Things had become complicated very fast.

John snorted. Since when had his life **_not_** been complicated?

He thought about it for a minute, Oh yeah since before he had left Earth to test his and DK's theory.

John reached the conference room and entered, he found Ben and Iliana waiting for him there.

They saluted smartly and stood at attention when they caught sight of John. As soon as John laid eyes on Ben, he started to glared at him with his '_I'm the Grand Admiral and you seriously screwed up_' look causing Ben to start to cringe in anticipation and shift nervously from one foot to another while Iliana took a step away form her husband.

John moved toward Ben until they were practically nose to nose, "If you were anybody else's son, I'd throw you out the airlock…" John paused for dramatic effect, "…Unfortunately you're mine," said John dryly, "Just tell me what you've done now," he continued as he pulled out a chair and slumped into it.

Ben swallowed nervously, "I talked to the humans on the ship. I explained to them who we are and what we wanted to know, they seemed to believe me after I introduced them to some of my non-human officers. They didn't mention anything of importance except something about a war with machines," Ben reported.

That grabbed John's attention, "Machines?" he prompted.

"Yes sir, they weren't very forthcoming when it came to details," continued Ben.

"Fine then. Go bring them here," John ordered.

Ben hesitated, and John repeated his command, "Go…scoot, go get them now," ordered John as he waved Ben away.

"Yes sir," Ben acknowledged smartly before leaving the conference room leaving John and Iliana alone.

Iliana smiled sweetly at John, "You're getting soft in your old age, old man," she said, playfully baiting her father-in-law.

John glared darkly at her, "You do realize I can demote you kitchen cook, don't you?" he retorted.

Iliana's eyes grew wide in surprise, "Uh…I think I had something to do now sir," she said as she hastily took her leave, leaving John alone in the conference room.

John leaned back in his chair and linked his hands behind his head as he smiled, satisfied that he could still scare his officers.

His lighthearted mood did not last long as he remembered what Ben had told him.

__

A war with Machines.

__

Its like something out of a Terminator movie, thought John darkly, "All that's missing is Arnie showing up and saying, 'Hasta la vista, baby'," said John out loud.

His thoughts became darker as he tried to imagine how it had occurred. His thoughts had not been this dark since just after he beat back the Nebari. During the course of the war the Scarrens had discovered that he had lost his wormhole tech and right after the Nebari invasion, they had attacked the newly formed United Multi-Species Hegemony of which they were supposed to have been a major member of. Eventually they had been beaten into complete submission with the help of a Scarren resistance that had wished to change the perceived image of their species as viscous veracious murders.

As he remembered the end of that conflict, he remembered what Scorpius had done then, as if it was yesterday:

**__**

/Flashback/

John groggily came to. He found himself lying on a metal bed, he tried to remember how he had gotten here. Scorpius had requested his presence about something he had discovered, he gone to the lab and walked in…then darkness had descended upon him.

"Ah, good you're awake now," came Scorpius's velvety voice.

John turned to face Scorpius, "Grasshopper, what happened?" he asked as he rubbed his head, he felt weird.

"Nothing, I have merely given you a **_gift_**," answered Scorpius innocently with a saccharine smile.

That grabbed attention, "What!" trepidation and a little bit of fear began to trickle into John's body as he stood and stared at Scorpius, "What did you do to me?" demanded John Crichton of his former nemesis.

"It was merely a solution to both our problems and agift to you and Aeryn Sun for my past transgressions against you and Aeryn Sun," explained Scorpius simply, "Humans are a short lived species when compared to Sebaceans…I have changed that for you."

"**_What_**!" screamed John. Anger fueled him as he ran, grabbed Scorpius and pushed up against the wall, "**_What the dren did you think…Why the frell did you do it?_**"

"Calm yourself John," began Scorpius calmly, "Think of this logically, you have changed this galaxy for the better, you have changed the Scarrens forever and yet I know that none of this matters to you. Only your family matters to you," he paused as he waited for his comments to sink in for John. "**_Aeryn Sun may live to be 250 cycles, would you leave her to live her life alone?_** She has already lost you once John, she would not survive loosing you a second time."

John let go of Scorpius and stepped back, shock/uncertainty rolling through his body. He stood there for several minutes just staring at Scorpius as if he had never seen him before, finally John set his jaw and said quietly "You're a bastard you know that don't you? I will always hate you for what you did to me and Aeryn, no matter what you do."

Scorpius nodded at John, "I would have it no other…" Scorpius paused and smiled evilly at John, "I believe that that has become a natural law of the Universe. If you did stop hating me the universe would implode!"

Horror spread across John's face at Scorpius's comment, "Now I know that we've been spending to much together! **_I'm starting to rub off on you!_**" John exclaimed unable to come to terms with this new revelation.

Scorpius merely continued to smile at John.

/End Flashback/

John came back to the present, he was sitting in a conference room waiting for Ben to bring humans to meet him.

__

Humans that were battling some type of machine race.

**__**

Humans that were going to explain to why Earth was a dead planet in ruins.

****

Author's Notes: Hope u like this chapter. Please Read and Review.


	11. Chapter 10 Meeting the Admiral

****

What the Hell happened here!

Disclaimer: I don't own the Matrix or Farscape

****

Author's notes: Your reviews were appreciated. Thanks! Here's the new chapter in record time! Read, Enjoy and Review! But don't expect the next update to be finished soon:( , sorry!

Grayangle: I looked in my heart and found this, so enjoy :)

Chapter 9 Meeting the Admiral

Meanwhile on the Neb, a very heated discussion was going on concerning their host.

"Are you sure we're still not locked into the Matrix?" asked Neo again.

"We're sure, Kat and Tank wouldn't be here if we were…no implants remember?" Trinity answered assuring Neo on that score.

"So he's the real thing?" Neo asked seriously.

"I don't know. I truly do not know…" confessed Morpheus, uncertainty arrayed on his face.

"Then we just met a group of Aliens?" exclaimed Neo.

"As far fetched a revelation as that is it is no more stunning than waking up from the dream world," Morpheus answered philosophically.

"I think it _is_," Neo disagreed.

"I got to agree with Neo on this one Morpheus," added Trinity, "This is…well…incredible! I didn't think it possible," she shook her head incredulously.

Morpheus looked from one to the other before saying any thing. "If it is true then…Then it will take getting used to…"

The appearance of Tank forestalled any more talk, "Hey guys, Captain Sun-Crichton's back," Tank had been keeping an eye on the docking bay from the cockpit of the Neb, "It looks like he want's to talk to us again," Tank reported.

The group looked among themselves, "Then let us go see what the Captain wants," ordered Morpheus before heading for the docking hatch.

The once more came out into the docking bay and found Captain Ben Sun-Crichton along with Commander Iliana waiting there for them.

"Greetings again," began Ben with a welcoming smile, "I hope you have had time to accept what I have revealed to you."

"We are willing to accept it for now as the truth, as far fetched as it may seem," answered Morpheus for the group.

"Good. The Grand Admiral sends his compliments and invites you to meet with him, on his Command Carrier," Ben relayed his father's invitation.

Morpheus eyed him, "Your Grand Admiral, your father, the human, John Crichton, correct?"

"Yes," was Ben's to the point reply.

"Will he be able to answer all of our questions?" Morpheus asked.

"Yes, to that as well. Also he has many questions for you." added Ben.

"I will be glad to answer any question he has to the best of my knowledge," answered Morpheus.

"Then if you will follow me, I'll take you to the Admiral," said Ben as he gestured in the relevant direction.

Morpheus turned to Tank, "You, Fio and Kat stay with the Neb and begin repairs while we talk to the Admiral," he ordered.

Ben cut in, "If you want I can have a team of engineers put at your disposal?" he offered kindly.

Morpheus turned to him before anyone else could answer, "No thank you. We can handle it," he was willing to talk to them but he did not trust them yet.

"As you wish," retorted Ben nonplussed, "If you'll follow me now."

They followed silently behind Ben as he and Iliana made their way out of the docking bay.

A few minutes later their short walk had brought even more surprises for the crew of the Neb. Along the way Neo had accidentally kicked one of the small critters that were rolling along the deck. The thing had backed away from him, twitted at him a couple of times and had apparently threatened him with its small pincer arm before going on its way once more. Ben had explained that it was called a DRD and they helped maintain Jalina's systems. The crew had naturally been nervous that little machines were running all over the ship but Ben had assured them that they were not independent but controlled by the pilot (him) and Jalina.

That had sparked even more curiosity in Neo when Ben had referred to Jalina as a person. So he'd asked Ben about it.

The answer had caused them all to stop midstep in disbelieving shock and astonishment.

"_You mean to tell me this **ship**, is a **living sentient organism**!_" demanded Neo shakily.

"Yes, she's a Leviathan-hybrid," answered Iliana simply.

The three humans looked uncertainly around themselves, _in the belly of the Beast_, that was their shared thought. Even as they watched the walls, began to look like the digestive tract of some giant extinct animal and the arches in the corridor like ribs. It was a very unnerving…for all of them.

They continued walking in silence afterwards.

Eventually they reached what appeared to be an airlock, which they passed through. They came out into a grey metallic corridor and Ben explained they had crossed over from Jalina to the Command Carrier.

The corridors here were more crowed and they passe by many different species, some they had been introduced to and some that were new to them.

They came to a door and Ben gestured for them to enter behind him.

Inside the room was a brown large round table that took up the middle of the room, black leather chairs were arranged around it and sitting at the head of the table was a man that was wearing a more decorative version of Ben's black and green leather uniform. He appeared to be of middle age with dirty blonde hair with white streaks in it that made the man look more distinguished. He had kind blue eyes and he radiated charisma.

He rose from his chair and introduced himself, "I'm Grand Admiral John Crichton…but that's a mouthful, so just call me John or Crichton as you wish," he came round the table to stand in front of the group. "Welcome to my ship," John welcomed while looking the three humans over.

"Thank you…uh, John. I am Morpheus, leader of the Human Resistance. These are my companions Trinity and Neo," Morpheus said, the Admiral seemed very friendly he thought.

"Well make yourselves at home and why don't we have a little chat, I hear the weather on Earth is different these days?" John said as he retook his seat at the head of the table, "Bengy, why don't you and Iliana go take care of your responsibilities while I talk to these good people," he directed at Ben and Iliana.

Ben and Iliana stood at attention and said, "Yes sir," before smartly leaving the conference room.

John turned back to the three humans and said, "And now it's just _us_ humans here," he smiled invitingly at his guests.

The crew of the neb just smiled politely back at the admiral amused at his weird approach to these first talks.

John leaned forward with a kind smile on his face, "Now could you please tell me…**_WHAT THE HELL HAPPENED TO EARTH!_** _When I left humans still ruled, it was green **and the sun still shone!** So it's been a few centuries or more but still…" _ranted the admiral, "Perhaps you could explain how all _that_ happened?" his tone was once more calm and collected.

The crew of the Neb exchanged glances, no matter how they explained he would not like what they had to say. Not one bit.

"Yes, we can explain all that but…" began Morpheus slowly.

"But what?" demanded John irritably.

Morpheus cleared his throat. "How do we know you are who you say you are?" he asked gravely.

John locked eyes with Morpheus, "You'll just have to believe me…just as I'll have to believe what you have to say," countered John easily.

Morpheus continued to return John's stern stare. He nodded, they both had to trust each other to find out what the other knew, "I will…for now," he said slowly.

"Fine then, are you going to explain now?" asked John testily.

Morpheus traded significant glances with Neo and Trinity then nodded again in affirmation, "I will. Years ago we built machines to help us…"

John leaned back into his chair listening intently to what Morpheus had to say.

An arn later Morpheus had explained a great deal and John was numb with disbelief/horror at the fate of his race.

****

The machines rebelled, the humans blotted out the sun and the machines turned the humans into walking batteries.

These thoughts repeated themselves in John's mind as every fiber of his being begged them to be mere figments of his imagination.

****

The human he had touched on Earth had been hooked up to the Matrix, powering the machines that had enslaved him.

But they weren't figmeif what Morpheus said was true and everything they had seen and scanned on Earth was supporting it.

__

While he and Aeryn had been living happily together, Humans had been fighting for their survival…**and failed.**

The guilt from that revelation threatened to overwhelm him, it spawned more questions that threatened to haunt him for the rest of his days. When had all this happened? Had his family still been around when this happened? Had the machines murdered them?

Slowly John painfully brought himself out of his reverie and back to the present.

He looked up at Morpheus, "How many humans are still free?"

Morpheus looked pained at this question, "Between the other resistance members and the inhabitants of Xion, almost 5 million."

John face grew white and he felt as if someone had just put a pulse pistol to his stomach and fired.

__

5 million? 5 million! 5 **MILLION**! THERE USED TO BE 7 **BILLION**_ ON EARTH! _his mind screamed in denial.

He collapsed back into his chair his body nerveless. _Why did the universe keep played with him like this? _he demanded angrily of Fate.

The three humans in the conference room with him exchanged concerned glances, "Admiral, are you all right?" asked Morpheus.

John turned eyes that blazed with burning emotion towards Morpheus, "As of now the complete resources of the United Multi-Species Hegemony Armed Forces are at your disposal. **_And I will make the machines pay for what they have done to my Race!_**" vowed John Crichton vehemently to the leader of the Human Resistance, as his blood screamed for Vengeance and Freedom for his homeworld.

****

Author's Notes: Hope u like this chapter. Please Read and Review.


	12. Chapter 11 The Next Step

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What the Hell happened here!

Disclaimer: I don't own the Matrix or Farscape

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Author's notes: Your reviews were appreciated. Thanks! Here's yet another new chapter in record time! Read, Enjoy and Review! But don't expect the next update to be finished soon, cause I'm starting exams soon.:( , sorry!

Calen: I did mention before that this story is AU after the first movie.

tatsu.zzmage: I've thought of that, haven't decided if I'm going to use is or not.

Worker72: Maybe, it's possible, but are Pilots able to interface with anything other than Leviathans? And besides if I did that then the story would be over in a couple of chapters.

Alatioc01: The machines are a couple of steps away from having a coronary (or its equivalent), I'll probably put that in the next few chapters. And I do plan to have John visit the Matrix, there's going to be a hell of a surprise waiting for him there:) , but not sometime soon.

Darklight: He isn't the old Crichton, he's changed and more mature.

Chapter 10 The Next Step

The three members of the Human Resistance exchanged glances before looking at Admiral John Crichton.

"What are you going to do?" asked Neo tentatively.

John surged out of his chair and turned to him, eyes still blazing with emotion, "I will do anything necessary to free humanity! If I have to level every machine city to bedrock, then…**_that is a step that I am willing to take_**!" John explained vehemently.

"Wait a minute! There are billions of humans trapped in the Matrix! You just can't slaughter them all!" argued Trinity, her mind reeling at the possible death toll of such an action.

"What! There are billions trapped in the Matrix?" demanded John of her. He turned to Morpheus, "You never mentioned that! Didn't you think that was worth mentioning before?" he now demanded of Morpheus.

Morpheus regarded John, nonplussed, "I was going to explain that detail once, once you proved to us who you are," Morpheus said evenly.

John eyed Morpheus before cursing, "Damn, I forgot how paranoid my people can be. Ancient Jack was so frelling right. You want proof? Fine. What can I do?" asked John of the dark skinned human.

"How about a DNA analysis for starters? We have the facilities on our hovercraft," suggested Morpheus forcefully.

"Fine." said John, he touched the comm on his shirt, "We're heading over to Jalina."

Morpheus looked at John in confusion, not knowing that it was a comm. John was answered by a short guttural clicks and clacks.

"Follow me," commanded John Crichton.

As they followed the Admiral out of the conference room they were met with four hulking calcivores that were the Admiral's bodyguards, each one even bigger than the one Ben had introduced the humans to.

The humans followed along in the Admiral's wake barely keeping up with the John's fast paced walk. In no time at all they found themselves back at the airlock which John and his escort briskly entered, while the humans hesitated slightly as they reentered what the had nervously though of as the belly of the beast.

Finally they reached Jalina's docking bay and the Neb. John paused a few meters away from the craft and turned towards the humans, "Well lead the way and lets get this over with, we have a planet to free form Machine domination," said John testily.

Morpheus ignored the pointed remark and moved to the Neb's airlock, input the entry code and pulled the door open. He turned to gesture for John to follow him and then entered.

Morpheus headed for the medical bay, Tank and Kat were working in the hall leading to the bay.

Tank stopped what he was doing looked at Morpheus and noticed the expression on his leader's face, "Morpheus, what's going on?" he asked.

"Just stay out of the way Tank. You too, Kat," Morpheus ordered tensely.

Tank and Kat exchanged glances as Morpheus moved past them. Their eyes grew wide as they took in the hulking calcivores that came next surrounding the important looking human that bore a striking resemblance to Ben Sun-Crichton, who also ignored them as he passed the duo of working humans. Trinity and Neo came in the wake of the aliens.

"What's happening?" demanded Kat of them.

"Follow us and find out," said Trinity quickly.

"Trust me you want to come see this," added Neo just as quickly.

Tank and Kat exchanged bewildered glances before following.

Morpheus had reached the medical and bay. He brought out a syringe and turned to John, "Roll up your sleeve and hold out your arm," Morpheus tensely commanded.

"Sure doc, whatever you say," John muttered as he rolled up his sleeve, exposing his flesh up to the elbow, "Just be sure to really jab it in," commented John sarcastically as Morpheus came at him.

Morpheus smiled sarcastically at him, aimed the needle at the brachial artery and gently eased the needle into John's arm. Slowly he extracted a few milliliters of blood from John.

"Done," said Morpheus, "It'll take the scanner a few minutes to analyze the DNA," he said as he moved to place the vial of John's red blood in the scanner.

John held his thumb over the where the needle had pierced the skin, "What no cotton balls to wipe this?" he added sarcastically.

"Sorry we're all out," said Morpheus with a sarcastic smile, in the same sarcastic tone as John.

The rest of the occupants of the now extremely cramped and crowded medical bay watched with trepidation as the two great men threw sarcastic remarks at each other.

Morpheus stood in front of the screen that would display the results once the machine had finished scanning the Admiral's DNA. He waited listlessly. If the Admiral was truly what he said he was then things had finally started to look up for the Human resistance and perhaps he would even get to see the end of the war in his lifetime. It was his lifelong wish, ever since he had woken up from the dream world.

__

And it all depended on the outcome of this analysis…

The minutes passed by as hours for all.

The scanner beeped and brought Morpheus out of his reverie. He gazed at the screen and read what was displayed. He blinked. He read it again. He swallowed and turned slowly to face the Admiral as hope for the future threatened to overwhelm him, "I…I believe I owe you an apology for my curtness Admiral and…Welcome Home."

John smiled smugly, "Apology accepted and thank you."

Morpheus said to the rest of his crew, "He is who he says he is."

The humans exchanged glances, wondering what was going to happen now.

"Perhaps now we can discuss what we have to do to free humanity?" asked the Admiral evenly of Morpheus.

"Yes, I believe we can now do that," answered Morpheus slowly. He turned to his fellow humans, "I believe the machines are about to…live in interesting times as the Chinese say."

"Amen to that, my new friend," added John with a smile as he contemplated how much he was going to make them pay.

Hours later, things had radically changed for the crew of the Neb. After the results of John's DNA test had been seen, John had insisted that the entire crew of the Neb under go exams by the hegemony docs and receive translator microbes so they could talk to the aliens. The medics practically wet themselves with excitement at the prospect of examining other humans, it become very disconcerting for the humans near the end. The Neb had been completely repaired and now Tank, Kat and Fio were working with some Hegemony techs to upgrade some systems, add some Hegemony weapons and introduce Earth VR and computer-mindlink technology to the Hegemony techs.

Meanwhile, Trinity, Morpheus and Neo had been discussing what course of action to follow, especially what to do with the billions of humans locked into the Matrix. But one thing was certain; John was adamant that he visit Xion, first, before they did anything drastic and before they took the war to the machines. This trip would also have another objective; supply the people with much needed medicines that they were unable to make in sufficient quantities there. John had also taken the time to introduce them his senior captains.

So by the end of the day, it was a very weary John Crichton that finally dragged himself into his quarters. Aeryn was lying in bed talking with her d, Zhaan when they heard the outer door open, the twins were peacefully sleeping in the other room and their new nanny, a middle aged Delvian woman was listening in on them in case they awoke during the night. They both heard as John cursed quietly when he accidentally walked into one of the low tables they had had in the anteroom of their suite of rooms on the Command Carrier.

"We really got to do something about that table Aeryn. Everyday, _everyday_, I walk into it. One of these days I'm going to pull out my pulse pistol and blast!" said John disgustedly as he walked into the bedroom.

"You mean like the last one you blasted, dad?" asked Zhaan sweetly.

"What? What are you doing here Zhanny? Shouldn't you still be on duty?" asked John in surprise, "And No I did not blast the last one," he answered adamantly.

"Yes you did John, it took maintenance a week to get the char marks out of the carpet," corrected Aeryn with a smile.

John gave her a betrayed look and said, "Why do you have to correct me?"

Aeryn pursed her lips as she thought about it, "Because I can?" she finally answered.

John glared at her for that comment then turned to glare at Zhanny as she giggled at her mother's comment.

"Uh, Zhanny what are you doing here?" John asked again.

"I'm just talking to my mother what does it look like?" she said innocently.

"About?" John asked simply.

"We were just discussing the humans…and a little girl talk," Zhaan said.

"Really…Anything I should know?" asked John interestedly as he flopped into one of the chairs in the room.

"Not really, just that the female techs are taking bets about who can bag that big muscular human, you know the one called Tank," said Zhanny offhandedly.

"Really? Not Neo? I would have thought they would be more attracted to Neo," asked John in surprise.

"Oh they are, it's just that Neo's apparently dating Trinity," replied Zhanny.

Aeryn had been watching them talk, "Zhaan, why don't you leave us now, your father looks like he's about to fall asleep where he's sitting," she suggested.

"Sure, as you wish," Zhaan said as she rose and moved towards her father, "You do look tired dad, get some sleep, I have a feeling tomorrows going to be a long day," she said. She gave him a kiss on the cheek, "I'll see you both tomorrow," and with that she left them alone.

They sat in silence for a few moments before Aeryn said, "What's wrong John? What's bothering you?"

"Nothing's bothering me sunshine," denied John.

Aeryn gave him a very pointed look, "John, you may have fooled Zhaan and everyone else but not me. I know you too well."

John didn't answer, instead he got up and lay on the bed next to Aeryn looked up at the ceiling, "Everything's gone Aeryn," he said quietly, sadness clouding his voice.

Aeryn looked unhappily at John, "We've know that for some time John," she said as she curled up next to him with one arm stretched across his chest, which she used to stroke his face.

John pulled her closer to him before answering, "I know…but it's all sinking in now. No matter what we do now…**_Earth is gone_**. The planet's to for gone for anything to change it back. **_It's a dead rock now_**," John said despondently.

"But humanity isn't…" began Aeryn, trying to comfort her husband.

"It almost was. They can't hold out for much longer," John said as despair threatened to overwhelm him.

"Yes, but we're here now. It's all going to change now, we can save them…you can save them," Aeryn said quietly.

"Yes…Yes I can. And I will," John confirmed, "I saved everyone else, why shouldn't I be able to save my own kind?"

Aeryn lifted herself up enough to give him a kiss, then she looked directly into his eyes and said, "You will John, _you will_."

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Author's Notes: Hope u like this chapter. Please Read and Review.


	13. Chapter 12 Points of View

**What the Hell happened here!**

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**Disclaimer: **I don't own the Matrix or Farscape

**Author's notes: **Your reviews were appreciated. Thanks! Read, Enjoy and Review! This chapter will merely be a few interludes to catch some characters reactions and give a little background to how the United Multi-Species Hegemony works-More Sun-Crichtons are on the way!J Anyway interlude one is an homage to one of my favorite scenes from the Matrix: Revolutions. We'll get back to the main storyline either in the next chapter or the one after that, so enjoyJ

**Marz1: **Yes this does take place after the Peacekeeper Wars. As for going into the Matrix, well that's a few, maybe several chapters off.

**Kin Pandun: **That's the kind of review that makes a writer's dayJ Thanks!

**Grayangle: **-big grin- here's more;)

**Worker72: **Maybe, but if I did that this story would be over in the same chapterL Also do you actually think that John is in a bargaining mood?

Chapter 11 Points of view Interlude 1 

It was the next day after the meeting with Grand Admiral John Crichton and Trinity was standing in one of the gardens on the Command Carrier, for the first time in her life standing in the light of Earth's sun. She could close her eyes and feel the sunlight playing over her face, it was a sensation she had loved when she was a child still locked in the dream world…but this was the first time she had felt that feeling in the real world.

She remembered when Zhann had first shown her this garden, to say she had been surprised to find a garden on a spaceship was an understatement. To then see the sun shining down at her and feel the sunlight playing across had taken her breath away and for several minutes all she could do was stand there looking at the sun she had so cherished in her youth in the dream world…

"Trinity, are you all right?" Zhann had asked uncertainly after waiting there for a reaction from the human woman.

Trinity had swayed as if she hadn't heard Zhann's question but she had answered her after a few silent minutes had passed, "It's just…I've never seen the sun before…I've never felt its rays play over my skin before…" Trinity said in an emotional charged tone.

Zhann looked into Trinity's eyes and saw amazement at such a small insignificant thing that she herself and billions of other in the Hegemony took for granted every single day of their lives.

Trinity now lay in the garden taking in the view that had so captivated her when she was young.

Interlude 2 

On the capital world of the United Multi-Species Hegemony, Terra Firma, named for the birthplace of Humanity and the Ancestors of the Sebaceans, another of the Sun-Crichtons sat at her desk trying to keep the planet running smoothly in her parents' absence.

She was the 80 cycle year old governor of Terra Firma, Samantha Sun-Crichton, the ninth offspring of Aeryn Sun and John Crichton. She was tall and took after her mother in attitude but after her father in coloring. She had pale blue eyes and long dirty blonde hair on Aeryn Sun's slim well built athletic body. Her office was situated in the top level of the Governor's building next to the Senate building. Both overlooked a nearby lake and the hero's memorial. Samantha's office had a spectacular view of the entire area.

On this day the headache that had started on the day that her parents had gone off on yet another search for Earth was still present and was only getting larger every day they were gone.

Every few years since their part of the galaxy had calmed down, her father would think that he had finally pinpointed where Earth was…and so far he had come up empty.

Every time there would be a fanfare and parades and speeches about how he was going home and going to bring humanity to the stars and introduce them to their brethren, the Sebacean people. And every time he was gone for a few months (once he was gone for a year) and they would find nothing. No sign of Earth or humanity. None at all.

In the mean time, while her father was on his pleasure cruise numerous bushfires all across the Hegemony would start burning, each one requiring a delicate touch by their diplomatic corps and each one screaming for the impartial view only her father could give them.

Samantha sighed and reached into her top drawer for the 'anti headache whammy', as her father called the analgesic. She pulled out two from the bottle and swallowed them whole without any water.

The headache started to abate immediately and she let out a sigh of relief, without these things her head would have exploded decades ago.

Each time she tried to look on the bright side, at least this time he took Ben and Jalina with him…that was one less headache she had to deal with. He was her brother and she loved him but sometimes she wanted her father to magically summon up a wormhole and shoot Ben and Jalina into it.

The other side of the galaxy should be enough insulation between them and the Hegemony.

Dealing with her father was tiring enough most of the time. She wondered how her mother had managed to put up with him for so long.

On the other hand, she wondered why they couldn't have taken the Ice Queen with him. Her big sister down right intimidated her…and not in a good way. Everyone agreed that calling her Xhalax had been a mistake. Even her father couldn't understand why her mother had been so insistent that they name their first daughter after that cold blooded monster.

Samantha shook her head, _at least she doesn't cause any trouble…_she thought wryly, _fact is, most people can't even look Commander 'Ice Queen' Xhalax Sun-Crichton in the eye without flinching and that helps prevent trouble._

Samantha shook herself out of her revere and tried to pay attention to the paperwork she had to finish today.

Before she had managed to finish the first line of the page in front of her, her female Nebari aide came barging into her office.

"Sam, Sam!" screeched Karia, "They found it!" she proclaimed breathlessly.

Samantha rose from her chair and opened her mouth to reprimand her aide for the interruption but that reprimand died still born on her lips and she froze as she assimilated the news that Karia had exclaimed. _They found it?_ "They found it?" she asked in disbelief.

Karia nodded confirming her statement.

Samantha collapsed boneless back into her chair and she ran the news through her mind. _They found it? They found it. THEY FOUND IT!_

Her breath came raggedly as she tried to understand what this could mean to her father, her family, Sebaceans everywhere and the Hegemony as a whole.

A million things needed to be down now and she straightened up and looked at her aide forming into words what needed to be done today…now before anything else.

She froze as she noticed that Karia wasn't just excited she was quivering…and not just with excitement, she appeared fearful.

"What is it?" Samantha asked with trepidation.

"Yo…your father…Admiral Crichton…he's ordered all forces to stand by. He's ordered ground assault vehicles and elite shock troops to Earth," she stammered in shock, she lowered her voice and whispered, "He's also asked for empty troop transports to be sent to him immediately!"

Samantha was stunned, _what had gone wrong?_

Karia wasn't finished, "He didn't go into details. He says it's too sensitive to send. There's a courier on his way now with the relevant information. He should arrive in a couple of weeks… " Karia said to the stunned Samantha.

Something struck her and Samantha snorted and kicked herself, how could she assume that contact with Earth was going to go off without a hitch?

Murphy himself lived there!

Interlude 3 

As far as Zhann was concerned these humans were turning out to be one surprise after another.

She was lying on her bunk in her quarters and idly reviewing what she had experienced in the last few days.

She'd been surprised at Trinity's reaction to such a simple thing as a sunrise in the gardens of the Command Carrier.

She'd been surprised at how Tank had gaped in awe at all the different species among the ranks of the Hegemony crew and the open mouthed expression that her mother swore had lived on John's face for a full cycle.

She'd been surprised by how much Neo seemed to brood…she'd never encountered or imagined a human could brood that much.

She'd never imagined that Morpheus could change from confrontational to helping in such a short time, but he had. Her father had told her that Morpheus now held a grudging respect for her father after hearing some of the things that had occurred during John Crichton's first few cycles in the Uncharted Territories.

Her father had nominated her as liaison between the crew of the Nebuchanezzer and the Hegemony forces. She'd spent the most of her time introducing them all to Hegemony tech. Most of the time she was sitting and talking with the human male Tank. In fact she'd been spending so much time with him that the other females on the Command Carrier had started to talk. She'd caught some of the female techs giving her envious glances…

Tank had enjoyed spending time with her and Zhann had to admit she wouldn't be adverse to something developing between them…

Zhann smiled to herself, he was pleasing to look at especially after they got him cleaned up and into better clothes than the torn ones he had been wearing.

She turned over in her bunk and with that pleasant thought in her head she drifted off to sleep, though one thing troubled her would he mind that she was sixty six cycles old? And old enough to be his mother?

**Author's Notes: **Hope u like this chapter. Please Read and Review. Expect our heroes to reach Xion soon.


	14. Chapter 13 Surprises in the Making

**What the Hell happened here!**

**Disclaimer: **I don't own the Matrix or Farscape

**Author's notes: **Your reviews were appreciated. Thanks! Read, Enjoy and Review! This isn't a proper chapter; this is just something for you to read to know that I haven't abandoned this story. More updates are still a ways off. SorryL

**Chapter 12 Surprises in the making**

The Oracle stood in her kitchen in the Matrix with the children she took care of. In recent months, she had felt a change in the Matrix, in the way that data flowed through it.

Data moved at a much faster pace now, between parts of the Matrix and its Agents. One could almost say the pace was more frantic in nature now.

And she knew why, the Oracle mused. Oh, she knew why, oh yes indeed; a new variable had been added to the computations of the Matrix. One that she knew they wouldn't be able to accurately predict to any usable degree, or at least not by their standards.

The Oracle smiled happily, the Machines' evil rule was nearing its end…she could feel it in her bones. All her work and effort these past centuries were about to come to fruition.

And 'he' would be coming to visit her here, soon. Yes, John Crichton would come see her soon…and oh, how she'd missed him, terribly all these long centuries. It would truly be good to see, both, him and Aeryn after all this time.

The Oracle turned to the children and said merrily, "Well what shall we bake today?"

xoxoxoxoxxoxoxoxoxoxoxoxoxoxoxox

To an outside observer, the Matrix may seem to be working diligently applying itself to solving its newest set of problems; dealing with the unknown Interlopers, in actual fact it was in a frenzy and about two steps away from panic.

The new modifications to the existing Sentinel design while they had verified to be very effective against the Human Resistance ships, had proven utterly ineffectual against the strange organic ships that had appeared, never mind the giant monstrosity that had then appeared and smashed the Sentinels as a human would swat a fly…with a twenty pound hammer.

Plans were already in motion to deal with failings of the Sentinels design, new model defenders were being designed, and the old Sentinel production sites were being retooled to mass-produce the new more powerful models. Hopefully the new design would prove to be a match worthy of dealing with the Interlopers.

The failings of the Sentinel design aside, there was one other thing that was causing feelings of trepidation and even fear to ripple through the Matrix; the fact that a Human Resistance ship had been engulfed by the giant monstrosity that had appeared in the end.

The Machines didn't know how this would affect the outcome of this conflict, but the Matrix's feelings could be summed up in one phrase;

'_I have a bad feeling about this…'_

xoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxox

Down in the last free city of Earth humans, Xion, the Commander of the city's defenses was contemplating the new changes in the armaments of the Sentinels, the disappearance of the Nebuchanezzer, and the strange ships that had been sighted during the last few months.

To new Sentinels were catastrophes as far the Commander was concerned, the one ship to first encounter them had been the Endeavor, and it had barely survived! The repairs were still ongoing and there was even the possibility that it would have to be scrapped. And Xion couldn't afford to lose any of their hovercraft. That coupled with the subsequent disappearance with of Morpheus and the others had caused morale to hit an all-new low.

The disappearance of the One was hitting the entire population of Xion, even though he didn't believe the prophecy, he still knew that having Neo around had breathed new life into all of Xion's forces…new life and hope that they all desperately needed.

The Commander's thought turned to the unknowns, the only thing they knew about them was that they had utterly trashed a swarm of Sentinels. More Sentinels than they had destroyed in the course of the entire war.

The Commander was a pessimist and he hoped and prayed that they weren't only going to try to destroy Xion. One of his subordinates, a rescuee from the Matrix had hopefully suggested the possibility that they were Humans who had fled Earth before the Machines had annihilated the rest of Humanity.

The Commander snorted in derision at the absurdity of such a theory. He didn't believe that, that theory was as absurd as another one he had heard spread among the men and women under his command; that Aliens had come to Earth.

The Commander shook his head, he could do nothing about that…all he could do was think of ways to strengthen Xion's perimeter defenses.

He turned back to his work.

xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox

"You see I told you it was spectacular," Trinity said in her told you so voice to Neo.

Neo smiled at her, "I've see it before…though I guess technically this is the first time I'm really seeing it," he admitted to her.

They were in one of the Farscape II's gardens watching the sunrise over Earth. Trinity had dragged Neo there that morning and set up an impromptu picnic for them. They were sitting on the grass, holding each other, Neo, behind Trinity.

"That makes it all the more spectacular," she muttered happily. For the first time in the Real world she felt happy and safe.

Neo kissed the top of her head, "It certainly does," he whispered quietly into her ear.

The modifications to the Nebuchanezzer were on schedule, the hovercraft would be more powerful than ever now, and everything was going great.

From Neo's perspective everything was perfect…he even could finally see the glimmer of hope for Humanity that others had said existed.

**Author's Notes: **Hope u like this chapter. Please Read and Review.


	15. Chapter 14 The Joys of Returns

**What the Hell happened here?!**

**Disclaimer: **I don't own the Matrix or Farscape

**Author's notes: **This story is NOT dead..._not yet anyway_. Your reviews were appreciated. Thanks! Sorry its been soooo long, I just truly dislike-hate the Matrix, but this is the only Farscape/Matrix cross on the net so it MUST be finished. And it will be. Just don't expect me to prolong this story any more than necessary.

Anyway now onto the story!!!:) Read, Enjoy and Review!:)

**Chapter 14 The Joy of Returns**

Frowning, Commander Lock paced back and forth in his office in Zion's defence command station, he paused for a second at the window that overlooked the city, a grim reminder of the what he and all the other's that had called the office theirs had to protect.

His frown deepened, a month ago Morpheus and the One's hovercraft had disappeared, Zion had undergone a terrible transformation. He had watched as the people's morale slowly slid downwards towards the abyss of uncertainty.

One month ago the Nebuchadnezzar had disappeared with all hands, without even a garbled distress call, the hovercraft had completely vanished, taking with it the people's perceived last remaining great hope that was Neo, thought Lock derisively.

He snorted, as if one man was enough to make the machines tremble in their metaphorical boots.

He continued pacing, angrily cursing Morpheus for believing the Oracle and her unbelievable unrealistic prophecies.

A tone form his desk interrupted his brooding, he touched a key and said, "This is Lock."

"Commander, sensors have picked out multiple hovercrafts on approach!" reported the sensor officer on duty excitedly.

"I thought we didn't have any crafts out at this time?" Lock asked in confusion.

"We don't sir! The lead craft looks like the Nebuchadnezzar!"

"What?! Confirm that!" Lock demanded.

"They'll be in range in a five minutes, but all preliminary scans say its Morpheus's ship!"

"Stand by, I'll be right down."

xoxoxoxoxoxoxoxoxoxoxoxox

A few short moments later, Lock entered the cramped Command centre to find a vision of controlled chaos as various on duty techs ran around making sure that the equipment was functioning properly.

The sensor officer quickly waved the Commander over, "Sir, I've gone over the images three times already. They've transmitted the clearance codes and are T minus 5 minutes from entering the docking yards. There's no doubt about it sir, its the Nebuchadnezzar." He announced in breathless excitement. He paused for a second before continuing, "Sir, Morpheus also says they're not coming in alone."

Lock kept his face blank, "Establish communications, get me Morpheus-now!" he called out.

"Yes sir!" another tech jumped to obey.

"This is Zion Control calling the Nebuchadnezzar, over," the tech spoke into a microphone.

They waited for a several very long minutes before they received an answer.

"This is Morpheus, go Zion Control," Morpheus's arrogant voice came over the speaker setting Lock's teeth grinding.

"This is Lock, What the hell is going on? Where the hell have you been and what's this about bringing company with you?" Lock demanded irritably.

"Commander Lock, its good to hear your voice again. Yes we have encountered something... unexpected. Suffice it to say we have friends following us in, they came bearing much needed materials and medical supplies."

Confusion reigned in Lock's mind, "Supplies? Unexpected how?"

"I do not wish to speak over an open channel, there will be ample time to speak once we have landed. Understand this Commander Lock, the stalemate has been broken, we are no longer alone."

xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox

Down in the docking yards, cheering crowds gathered as the hovercraft came in for a landing. People that had seen their last hope taken from them just as quickly as it had appeared saw it returned just as quickly.

News of the Nebuchadnezzar's return had spread like wildfire from techs in the command centre to dock workers and the inhabitants of Zion. People of all ages flocked to greet and welcome them back and to find out where they had been for the last month.

Those watching saw as it gracefully descended for a landing, noticing nothing and seeing nothing other than their heroes returning home.

Commander Lock, security officers and Dockworkers watched as a much changed Nebuchadnezzar came in for a landing. It was sleeker, less angular than before and had a much newer darker paint job than when it had left the city a month ago.

With a slight bump, the Nebuchadnezzar landed in its slipway, and the boarding ramp descended a few moments later as lights started to flicker off, signifying the pilot shutting down the hovercraft.

The cheers of the crowd that had intensified as the hovercraft landed stilled and silence descended as a figure appeared at the top of the boarding ramp.

The figure walked out into the light.

Lock blinked and the security officers with him tensed as an unfamiliar figure in a black green and red uniform walked idly down the ramp as if he hadn't a care in the world.

"Aw shucks, you shouldn't have," said the man in a southern drawl, flashing them a big smile.

"Who are you?" Lock demanded.

"Me? The name's Grand Admiral John Crichton of the Multispecies Hegemony and I'm here to save you..."

He said with a smug smile.

Another figure in full black body armour quickly came down the ramp before Lock could think of a proper response and spoke in a foreign language to the Admiral.

The helmeted man spoke what was to Lock's ears, gibberish.

The Admiral just gave him a pointed look.

The helmeted man's shoulder slumped in defeat, and didn't say anything.

"I thought we said you where going to wait?" Neo asked as he walked down the ramp. "Commander Lock, its been a while." he greeted Lock.

Lock gave Crichton a look before turning to Neo, "Where's Morpheus? And who's this?"

Neo opened his mouth but Crichton beat him to it, "Hard of hearing is he?"

Lock bristled but Neo quickly cut in, "This is Admiral Crichton, basically he left Earth a long time ago and now... he's back, with friends I might add." Neo stressed the friends part.

Lock blinked, not comprehending, "What do you mean friends?"

"Aliens, lots and lots of Aliens. That clear enough for you?" Crichton said snidely.

Lock's jaw dropped in surprise, "That's impossible!"

"Many things once thought impossible are now possible," proclaimed Morpheus as he walked down the ramp to join them. "We have much to discuss with the Council, we should adjourn to the council chamber."

Lock stared at his old rival, "This way."

xoxoxoxoxoxoxoxoxoxoxoxoxox

For the first time in a century John Crichton walked through a human city... and boy did he not like what he was seeing.

They'd started out as a small group heading out to Zion's Council chambers. The other members of the Council were already awaiting them there. As they walked, they gathered silent observers. People of all ages gathered to watch the strange silent procession. Known Leaders of the Human Resistance forces walked with a half dozen strangers in clean well pressed uniforms and full body armour. They surrounded a single older man in a decorated uniform.

John Crichton looked at the people; men women and children of all ages, all carried the same haunted almost broken look on their faces. The tattered rags they all wore spoke of the decrepit nature of their lives. Malnourished children paced the group as they moved forwards.

The actual state of the city matched the state of the people, the city looked like it had been built inside one massive cave or group of connected caves. The buildings grew from the floor of the cave upwards to meet the stalactites .

Layered apartments, that's what all these building looked like, the same design, over and over again, trying to accommodate the last dregs of an almost extinct race.

In a dark part of his mind he promised himself that he would do everything in his power to change the lows that humanity had fallen to...and they had fallen very far indeed.

Earth was dead, but as long as he lived so would Humanity!

**Author's Notes: **Hope u like this chapter. Yes this story is still alive. Don't forget to Review.


	16. Chapter 15 Salvation

**What the Hell happened here?!**

**Disclaimer: **I don't own the Matrix or Farscape

**Author's notes: **Read, Enjoy and Review!:) Hopefully the next chapter won't be such a wait :) Keep your fingers crossed!:)

**Chapter 15 Salvation**

Crichton stood in the centre of Zion's council chamber gazing all around himself at the dozen assembled elders of the city, the leaders of the the last machine free city on Earth.

Though as a council chamber it didn't live up to the grandiosity of its name. It was a simple large hall with a wide table with enough places for the twelve members of Zion's council.

The places were all filled now, the assembled council had hastily convened once word of the _Nebuchadnezzar'_s return had reached their ears. The rumours that had sprung up like wildfire and travelled through the population of Zion in record time, ringing in their minds, of newcomers and aliens and all manner of impossibilities.

These rumours had filled the minds of the council as they assembled in hurry to discern fact from superlative fiction. As they found out the fiction was was not as outlandish as the facts.

Over the course of an hour Grand Admiral John Crichton of the United Mutli-Species Hegemony had give them the gist of his story and a short history of the galaxy at large.

Heated arguments broke out over the veracity of his mad tale and if not for the heated intervention and hearty testimony of Morpheus and the others they would have continued to doubt Crichton's claims and aid.

John surveyed the gathered humans, many emotions played out on their faces though nearly all of them carried looks of shock on their faces. Some still stubbornly held on to their disbelief, while others had a looks of eager hope. In either case what he was about to say would provoke extreme reactions from both groups.

"In three months," John paused dramatically, "transport ships from the Hegemony will arrive in Earth orbit. These _empty_ ships will have enough room and provisions to totally evacuate Zion and transport you all to a suitable colony world in the Hegemony."

Silence descended upon the council chambers as the import of John's words rang in their minds.

John gazed around and caught the eyes of each council member, "The Hegemony will protect and aide this colony until such time as you can stand on your own feet and then...you can decide whether or not you wish to stand alone or formally join the Hegemony."

The council chamber erupted into an uproar.

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In the aftermath of Crichton's proclamation, Neo and Trinity retreated to their own private apartment. Lying together entwined on the bed they talked about Crichton's offer of nothing less than salvation.

"This is it isn't it?" Trinity asked.

"It?" Neo questioned in confusion.

"Crichton's saved us all hasn't he?"

"...it sure looks that way,but..."

"But what, Neo?"

"If Crichton's our saviour then what is the Oracle? And who's the one? Is it him? And-"

Trinity cut him off, "-how did she know about him?"

"Yeah...for starters."

"I...don't know Neo."

"You know if I hadn't seen everything with my own eyes, I'd think that this was all too good to be true."

"But it is true, they have the Numbers, Technology and Will to save us all," Trinity tried to reassure him.

Neo kissed the top of her head, "They do, but...this seems like a dream."

Trinity snuggled closer to him in response but didn't say anything.

"I just...want to understand the Oracle's prophecy, she said so much to us but now...so much of it doesn't make any sense," Neo said wistfully.

Trinity raised her head off of Neo's chest and looked up at him, "There's a simple solution you know? We could just go talk to her?"

**Author's Notes: **Hope u like this chapter. Yes this story is still alive(barely). Don't forget to Review.


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